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Sample records for pre-main sequence evolutionary

  1. THE HABITABLE ZONES OF PRE-MAIN-SEQUENCE STARS

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, Ramses M.; Kaltenegger, Lisa [Institute for Pale Blue Dots, Cornell University, Ithaca, NY (United States)

    2014-12-20

    We calculate the pre-main-sequence habitable zone (HZ) for stars of spectral classes F-M. The spatial distribution of liquid water and its change during the pre-main-sequence phase of protoplanetary systems is important for understanding how planets become habitable. Such worlds are interesting targets for future missions because the coolest stars could provide habitable conditions for up to 2.5 billion years post-accretion. Moreover, for a given star type, planetary systems are more easily resolved because of higher pre-main-sequence stellar luminosities, resulting in larger planet-star separation for cool stars than is the case for the traditional main-sequence (MS) HZ. We use one-dimensional radiative-convective climate and stellar evolutionary models to calculate pre-main-sequence HZ distances for F1-M8 stellar types. We also show that accreting planets that are later located in the traditional MS HZ orbiting stars cooler than a K5 (including the full range of M stars) receive stellar fluxes that exceed the runaway greenhouse threshold, and thus may lose substantial amounts of water initially delivered to them. We predict that M-star planets need to initially accrete more water than Earth did, or, alternatively, have additional water delivered later during the long pre-MS phase to remain habitable. Our findings are also consistent with recent claims that Venus lost its water during accretion.

  2. The Habitable Zones of Pre-Main-Sequence Stars

    CERN Document Server

    Ramirez, Ramses M

    2014-01-01

    We calculate the pre-main-sequence HZ for stars of spectral classes F to M. The spatial distribution of liquid water and its change during the pre-main-sequence phase of protoplanetary systems is important in understanding how planets become habitable. Such worlds are interesting targets for future missions because the coolest stars could provide habitable conditions for up to 2.5 billion years post-accretion. Moreover, for a given star type, planetary systems are more easily resolved because of higher pre-main-sequence stellar luminosities, resulting in larger planet to star separation for cool stars than is the case for the traditional main-sequence (MS) habitable zone (HZ). We use 1D radiative-convective climate and stellar evolutionary models to calculate pre-main-sequence HZ distances for F1 to M8 stellar types. We also show that accreting planets that are later located in the traditional MS HZ orbiting stars cooler than a K5 (including the full range of M-stars) receive stellar fluxes that exceed the ru...

  3. Lithium Depletion in Fully Convective Pre-Main Sequence Stars

    CERN Document Server

    Bildsten, L; Matzner, C D; Ushomirsky, G; Bildsten, Lars; Brown, Edward F.; Matzner, Christopher D.; Ushomirsky, Greg

    1996-01-01

    We present an analytic calculation of the thermonuclear depletion of lithium in contracting, fully convective, pre-main sequence stars of mass M 0.08 M_sun) and for constraining the masses of lithium depleted stars.

  4. Massive pre-main-sequence stars in M17

    Science.gov (United States)

    Ramírez-Tannus, M. C.; Kaper, L.; de Koter, A.; Tramper, F.; Bik, A.; Ellerbroek, L. E.; Ochsendorf, B. B.; Ramírez-Agudelo, O. H.; Sana, H.

    2017-08-01

    The formation process of massive stars is still poorly understood. Massive young stellar objects (mYSOs) are deeply embedded in their parental clouds; these objects are rare, and thus typically distant, and their reddened spectra usually preclude the determination of their photospheric parameters. M17 is one of the best-studied H ii regions in the sky, is relatively nearby, and hosts a young stellar population. We have obtained optical to near-infrared spectra of previously identified candidate mYSOs and a few OB stars in this region with X-shooter on the ESO Very Large Telescope. The large wavelength coverage enables a detailed spectroscopic analysis of the photospheres and circumstellar disks of these candidate mYSOs. We confirm the pre-main-sequence (PMS) nature of six of the stars and characterise the O stars. The PMS stars have radii that are consistent with being contracting towards the main sequence and are surrounded by a remnant accretion disk. The observed infrared excess and the double-peaked emission lines provide an opportunity to measure structured velocity profiles in the disks. We compare the observed properties of this unique sample of young massive stars with evolutionary tracks of massive protostars and propose that these mYSOs near the western edge of the H ii region are on their way to become main-sequence stars ( 6-20 M⊙) after having undergone high mass accretion rates (Ṁacc 10-4-10-3M⊙yr-1). Their spin distribution upon arrival at the zero age main-sequence is consistent with that observed for young B stars, assuming conservation of angular momentum and homologous contraction. Based on observations collected at the European Southern Observatory at Paranal, Chile (ESO programmes 60.A-9404(A), 085.D-0741, 089.C-0874(A), and 091.C-0934(B)).The full normalised X-shooter spectra are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/604/A78

  5. Are pre-main-sequence stars older than we thought?

    CERN Document Server

    Naylor, Tim

    2009-01-01

    We fit the colour-magnitude diagrams of stars between the zero-age main-sequence and terminal-age main sequence in young clusters and associations. The ages we derive are a factor 1.5 to 2 longer than the commonly used ages for these regions, which are derived from the positions of pre-main-sequence stars in colour-magnitude diagrams. From an examination of the uncertainties in the main-sequence and pre-main-sequence models, we conclude that the longer age scale is probably the correct one, which implies we must revise upwards the commonly used ages for young clusters and associations. Such a revision would explain the discrepancy between the observational lifetimes of proto-planetary discs and theoretical calculations of the time to form planets. It would also explain the absence of clusters with ages between 5 and 30Myr. We use the $\\tau^2$ statistic to fit the main-sequence data, but find that we must make significant modifications if we are to fit sequences which have vertical segments in the colour-magni...

  6. Pre-main-sequence isochrones -- I. The Pleiades benchmark

    CERN Document Server

    Bell, Cameron P M; Mayne, N J; Jeffries, R D; Littlefair, S P

    2012-01-01

    We present a critical assessment of commonly used pre-main-sequence isochrones by comparing their predictions to a set of well-calibrated colour-magnitude diagrams of the Pleiades in the wavelength range 0.4 to 2.5 microns. Our analysis shows that for temperatures less than 4000 K the models systematically overestimate the flux by a factor two at 0.5 microns, though this decreases with wavelength, becoming negligible at 2.2 microns. In optical colours this will result in the ages for stars younger than 10 Myr being underestimated by factors between two and three. We show that using observations of standard stars to transform the data into a standard system can introduce significant errors in the positioning of pre-main-sequences in colour-magnitude diagrams. Therefore we have compared the models to the data in the natural photometric system in which the observations were taken. Thus we have constructed and tested a model of the system responses for the Wide-Field Camera on the Isaac Newton Telescope. As a ben...

  7. Structure and Evolution of Pre-Main Sequence Stars

    CERN Document Server

    Schulz, Norbert S; Bautz, Mark W; Canizares, Claude C; Davis, John; Dewey, Dan; Huenemoerder, David P; Heilmann, Ralf; Houck, John; Marshall, Herman L; Nowak, Mike; Schattenburg, Mark; Audard, Marc; Drake, Jeremy; Gagne, Marc; Kastner, Joel; Kallman, Tim; Lautenegger, Maurice; Lee, Julia; Miller, Jon; Montmerle, Thierry; Mukai, Koji; Osten, Rachel; Parerels, Frits; Pollock, Andy; Preibisch, Thomas; Raymond, John; Reale, Fabio; Smith, Randall; Testa, Paola; Weintraub, David

    2009-01-01

    Low-mass pre-main sequence (PMS) stars are strong and variable X-ray emitters, as has been well established by EINSTEIN and ROSAT observatories. It was originally believed that this emission was of thermal nature and primarily originated from coronal activity (magnetically confined loops, in analogy with Solar activity) on contracting young stars. Broadband spectral analysis showed that the emission was not isothermal and that elemental abundances were non-Solar. The resolving power of the Chandra and XMM X-ray gratings spectrometers have provided the first, tantalizing details concerning the physical conditions such as temperatures, densities, and abundances that characterize the X-ray emitting regions of young star. These existing high resolution spectrometers, however, simply do not have the effective area to measure diagnostic lines for a large number of PMS stars over required to answer global questions such as: how does magnetic activity in PMS stars differ from that of main sequence stars, how do they ...

  8. The coronal evolution of pre-main-sequence stars

    CERN Document Server

    Gregory, Scott G; Davies, Claire L

    2016-01-01

    The bulk of X-ray emission from pre-main-sequence (PMS) stars is coronal in origin. We demonstrate herein that stars on Henyey tracks in the Hertzsprung-Russell diagram have lower $\\log(L_X/L_\\ast)$, on average, than stars on Hayashi tracks. This effect is driven by the decay of $L_X$ once stars develop radiative cores. $L_X$ decays faster with age for intermediate mass PMS stars, the progenitors of main sequence A-type stars, compared to those of lower mass. As almost all main sequence A-type stars show no detectable X-ray emission, we may already be observing the loss of their coronae during their PMS evolution. Although there is no direct link between the size or mass of the radiative core and $L_X$, the longer stars have spent with partially convective interiors, the weaker their X-ray emission becomes. This conference paper is a synopsis of Gregory, Adams and Davies (2016).

  9. The potential of space observations for pulsating pre-main sequence stars

    CERN Document Server

    Zwintz, Konstanze

    2016-01-01

    The first asteroseismic studies of pre-main sequence (pre-MS) pulsators have been conducted based on data from the space telescopes MOST and CoRoT with typical time bases of less than 40 days. With these data, a relation between the pulsational properties of pre-MS delta Scuti stars and their relative evolutionary phase on their way from the birthline to the zero-age main sequence was revealed. But it is evident from comparison with the more evolved pulsators in their main sequence or post-main sequence stages observed by the main Kepler mission, that many more questions could be addressed with significantly longer time bases and ultra-high precision. Here, I will discuss the observational status of pre-MS asteroseismology and the potential of future space observations for this research field.

  10. ACCRETION RATES ON PRE-MAIN-SEQUENCE STARS IN THE YOUNG OPEN CLUSTER NGC 6530

    Energy Technology Data Exchange (ETDEWEB)

    Gallardo, Jose; Del Valle, Luciano; Ruiz, Maria Teresa, E-mail: gallardo@das.uchile.cl, E-mail: ldelvall@das.uchile.cl, E-mail: mtruiz@das.uchile.cl [Departamento de Astronomia, Universidad de Chile, Casilla 36-D, Santiago (Chile)

    2012-01-15

    It is well accepted that during the star formation process, material from a protoplanetary disk is accreted onto the central object during the first {approx}1-5 Myr. Different authors have published measurements of accretion rates for young low- and intermediate-mass stars in several nearby star-forming regions (SFRs). Due to its somewhat larger distance, the SFR M8 (the Lagoon Nebula) has not been studied to the same extent, despite its abundant population of young stellar objects. We have obtained optical band low-resolution spectra of a sample of pre-main-sequence stars in the open cluster NGC 6530 located in the aforementioned nebulae using the Gemini Multi Object Spectrograph at Gemini-South in multi-object mode. Spectra cover the H{sub {alpha}} emission line used to measure the accretion rate, following the method presented by Natta et al. The observed spectral characteristics are fully consistent with pre-main-sequence stars, showing lithium absorption lines, which are very common in young stellar objects, as well as prominent and broad H{sub {alpha}} emission lines, indicating a T Tauri evolutionary stage. This work presents the first determinations of mass accretion rates of young stellar objects in the open cluster NGC 6530, confirming that they are classical T Tauri stars going through the accretion phase. These observations contribute to a better understanding of the stellar content and evolutionary phase of the very active Lagoon Nebula SFR.

  11. Pre-main sequence spectroscopic binaries suitable for VLTI observations

    CERN Document Server

    Guenther, E W; Mundt, R; Covino, E; Alcalá, J M; Cusano, F; Stecklum, B

    2007-01-01

    A severe problem of the research in star-formation is that the masses of young stars are almost always estimated only from evolutionary tracks. Since the tracks published by different groups differ, it is often only possible to give a rough estimate of the masses of young stars. It is thus crucial to test and calibrate the tracks. Up to now, only a few tests of the tracks could be carried out. However, with the VLTI it is now possible to set constrains on the tracks by determining the masses of many young binary stars precisely. In order to use the VLTI efficiently, a first step is to find suitable targets, which is the purpose of this work. Given the distance of nearby star-forming regions, suitable VLTI targets are binaries with orbital periods between at least 50 days, and few years. Although a number of surveys for detecting spectroscopic binaries have been carried out, most of the binaries found so far have periods which are too short. We thus surveyed the Chamaeleon, Corona Australis, Lupus, Sco-Cen, rh...

  12. The Effect of Pre-Main Sequence Stars on Star Cluster Dynamics

    CERN Document Server

    Wiersma, R; Zwart, S P

    2006-01-01

    We investigate the effects of the addition of pre-main sequence evolution to star cluster simulations. We allowed stars to follow pre-main sequence tracks that begin at the deuterium burning birthline and end at the zero age main sequence. We compared our simulations to ones in which the stars began their lives at the zero age main sequence, and also investigated the effects of particular choices for initial binary orbital parameters. We find that the inclusion of the pre-main sequence phase results in a slightly higher core concentration, lower binary fraction, and fewer hard binary systems. In general, the global properties of star clusters remain almost unchanged, but the properties of the binary star population in the cluster can be dramatically modified by the correct treatment of the pre-main sequence stage.

  13. Pulsation of Pre-Main Sequence Stars in Young Open Clusters

    Science.gov (United States)

    Zwintz, Konstanze; Weiss, Werner W.

    2001-08-01

    The aim of this proposal is to determine observationally the parameter space of the pre-main sequence instability strip. For that purpose we intend to obtain photometric timeseries with high time resolution and low noise level of the stars in young open clusters (IC 4996, NGC 6910 and NGC 6383) and to identify pre-main sequence pulsators. Several cluster members have the spectral types of interest (A-F) and lie between the birthline and the zero-age main sequence. Up to now the number of pre-main sequence pulsators is absolutely inadequate to determine reliably the hot and cool border of the according instability region. Its definition is indispensable for a better understanding of the internal structure and evolution of such stars.

  14. Theoretical seismic properties of pre-main sequence gamma Doradus pulsators

    CERN Document Server

    Bouabid, M -P; Miglio, A; Dupret, M -A; Grigahcene, A; Noels, A

    2011-01-01

    Context. gamma Doradus (gamma Dor) are late A and F-type stars pulsating with high order gravity modes (g-modes). The existence of different evolutionary phases crossing the gamma Dor instability strip raises the question of the existence of pre-main sequence (PMS) gamma Dor stars. Aims. We intend to study the differences between the asteroseismic behaviour of PMS and main sequence (MS) gamma Dor pulsators as it is predicted by the current theory of stellar evolution and stability. Methods. We explore the adiabatic and non-adiabatic properties of high order g-modes in a grid of PMS and MS models covering the mass range 1.2 Msun < Mstar < 2.5 Msun. Results. We derive the theoretical instability strip (IS) for the PMS gamma Dor pulsators. This IS covers the same effective temperature range as the MS gamma Dor one. Nevertheless, the frequency domain of unstable modes in PMS models with a fully radiative core is larger than in MS models, even if they present the same number of unstable modes. Moreover, the ...

  15. Low-mass pre--main-sequence stars in the Magellanic Clouds

    CERN Document Server

    Gouliermis, Dimitrios

    2012-01-01

    [Abridged] The stellar Initial Mass Function (IMF) suggests that sub-solar stars form in very large numbers. Most attractive places for catching low-mass star formation in the act are young stellar clusters and associations, still (half-)embedded in star-forming regions. The low-mass stars in such regions are still in their pre--main-sequence (PMS) evolutionary phase. The peculiar nature of these objects and the contamination of their samples by the evolved populations of the Galactic disk impose demanding observational techniques for the detection of complete numbers of PMS stars in the Milky Way. The Magellanic Clouds, the companion galaxies to our own, demonstrate an exceptional star formation activity. The low extinction and stellar field contamination in star-forming regions of these galaxies imply a more efficient detection of low-mass PMS stars than in the Milky Way, but their distance from us make the application of special detection techniques unfeasible. Nonetheless, imaging with the Hubble Space Te...

  16. A probable pre-main sequence chemically peculiar star in the open cluster Stock 16

    CERN Document Server

    Netopil, M; Paunzen, E; Zwintz, K; Pintado, O I; Bagnulo, S

    2014-01-01

    We used the Ultraviolet and Visual Echelle Spectrograph of the ESO-Very Large Telescope to obtain a high resolution and high signal-to-noise ratio spectrum of Stock 16-12, an early-type star which previous Delta-a photometric observations suggest being a chemically peculiar (CP) star. We used spectral synthesis to perform a detailed abundance analysis obtaining an effective temperature of 8400 +/- 400 K, a surface gravity of 4.1 +/- 0.4, a microturbulence velocity of 3.4 +0.7/-0.3 km/s, and a projected rotational velocity of 68 +/- 4 km/s. We provide photometric and spectroscopic evidence showing the star is most likely a member of the young Stock 16 open cluster (age 3-8 Myr). The probable cluster membership, the star's position in the Hertzsprung-Russell diagram, and the found infrared excess strongly suggest the star is still in the pre-main-sequence (PMS) phase. We used PMS evolutionary tracks to determine the stellar mass, which ranges between 1.95 and 2.3 Msun, depending upon the adopted spectroscopic o...

  17. EXPORT optical photometry and polarimetry of Vega-type and pre-main sequence stars

    CERN Document Server

    Oudmaijer, R D; Eiroa, C

    2001-01-01

    This paper presents optical UBVRI broadband photo-polarimetry of the EXPORT sample obtained at the 2.5m Nordic Optical Telescope. The database consists of multi-epoch photo-polarimetry of 68 pre-main-sequence and main-sequence stars. An investigation of the polarization variability indicates that 22 objects are variable at the 3sigma level in our data. All these objects are pre-main sequence stars, consisting of both T Tauri and Herbig Ae/Be objects while the main sequence, Vega type and post-T Tauri type objects are not variable. The polarization properties of the variable sources are mostly indicative of the UXOR-type behaviour; the objects show highest polarization when the brightness is at minimum. We add seven new objects to the class of UXOR variables (BH Cep, VX Cas, DK Tau, HK Ori, LkHa 234, KK Oph and RY Ori). The main reason for their discovery is the fact that our data-set is the largest in its kind, indicating that many more young UXOR-type pre-main sequence stars remain to be discovered. The set ...

  18. The Effect of Screening Factors and Thermonuclear Reaction Rates in the Pre-main Sequence Evolution of Low Mass Stars

    Indian Academy of Sciences (India)

    İ. Küçük; Ş. Çalışkan

    2010-09-01

    In understanding the nucleosynthesis of the elements in stars, one of the most important quantities is the reaction rate and it must be evaluated in terms of the stellar temperature , and its determination involves the knowledge of the excitation function () of the specific nuclear reaction leading to the final nucleus. In this paper, the effect of thermonuclear reaction rates to the pre-main sequence evolution of low mass stars having masses 0.7, 0.8, 0.9 and 1 M⊙ are studied by using our modified Stellar Evolutionary Program.

  19. Pre main sequence stars as UV sources for the World Space Observatory-UV mission

    Science.gov (United States)

    Gomez de Castro, Ana I.; Lamzin, Sergei A.

    2011-09-01

    Pre-main sequence stars are bright UV (UV) sources compared with their main sequence analogues. The source of this excess is the high energy processes associated with the physics of accretion/outflow during early stellar evolution. In this review, the main sources of UV excess are described as well as the most significant "unknowns" in the field. Special emphasis is made on the results from the last observations carried out with the Hubble Space Telescope and on the relevance of future dedicated monitoring programs with the World Space Observatory-UV.

  20. Differential rotation on both components of the pre main-sequence binary system HD 155555

    OpenAIRE

    Dunstone, N. J.; Hussain, G A J; Cameron, A. Collier; Marsden, S. C.; Jardine, M.; Barnes, J. R.; Vlex, J. C. Ramirez; Donati, J.-F.

    2008-01-01

    We present the first measurements of surface differential rotation on a pre-main sequence binary system. Using intensity (Stokes I) and circularly polarised (Stokes V) timeseries spectra, taken over eleven nights at the Anglo-Australian Telescope (AAT), we incorporate a solar-like differential rotation law into the surface imaging process. We find that both components of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) binary system show significant differential rotation. The equator-pole...

  1. Active phenomena in the pre-main sequence Herbig Ae star HD 163296

    Science.gov (United States)

    Catala, C.; Praderie, F.; Simon, T.; Talavera, A.; The, P. S.

    1989-01-01

    Observations by IUE of the short-term variability of the Mg II and Ca II resonance lines in the Herbig Ae star HD 163296 are presented. Evidence that these lines show a phenomenon of rotational modulation, similar to the one observed in AB Aur, another Herbig Ae star is found. The variations in the spectrum of HD 163296 are even more conspicuous than in the spectrum of AB Aur. Magnetically structured winds may thus be a widespread phenomenon among the pre-main sequence Herbig Ae/Be stars.

  2. Pre-main sequence variable stars in young open cluster NGC 1893

    OpenAIRE

    Lata, Sneh; Pandey, A.K.(Indian Institute of Technology Bombay (IIT), Mumbai, India); Chen, W. P.; Maheswar, G.; Chauhan, Neelam

    2012-01-01

    We present results of multi-epoch (fourteen nights during 2007-2010) $V$-band photometry of the cluster NGC 1893 region to identify photometric variable stars in the cluster. The study identified a total of 53 stars showing photometric variability. The members associated with the region are identified on the basis of spectral energy distribution, $J-H/H-K$ two colour diagram and $V/V-I$ colour-magnitude diagram. The ages and masses of the majority of pre-main-sequence sources are found to be ...

  3. Kinematic Distances of Pre-main Sequence Stars in the Lupus Star-Forming Region

    Science.gov (United States)

    Galli, P. A. B.; Teixeira, R.; Ducourant, C.; Bertout, C.

    2014-06-01

    The problem of the determination of distances has always played a central role in astronomy. However, little recent progress has been made in the distance determination of faint young stellar objects such as pre-main sequence (PMS) stars. Many of the PMS stars were neither observed by the Hipparcos satellite due to their magnitude nor have any trigonometric parallax measured from the ground due to their distance. Here we investigate the kinematic properties of the Lupus moving group with the primary objective of deriving individual parallaxes for each group member of this star-forming region.

  4. The first magnetic maps of a pre-main sequence binary star system - HD 155555

    OpenAIRE

    Dunstone, N. J.; Hussain, G. A. J.; Cameron, A. Collier; Marsden, S. C.; Jardine, M.; Stempels, H. C.; Vlex, J. C. Ramirez; Donati, J. -F.

    2008-01-01

    We present the first maps of the surface magnetic fields of a pre-main sequence binary system. Spectropolarimetric observations of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) system were obtained at the Anglo-Australian Telescope in 2004 and 2007. Both datasets are analysed using a new binary Zeeman Doppler imaging (ZDI) code. This allows us to simultaneously model the contribution of each component to the observed circularly polarised spectra. Stellar brightness maps are also produc...

  5. Differential rotation on both components of the pre main-sequence binary system HD 155555

    OpenAIRE

    Dunstone, N. J.; Hussain, G. A. J.; Cameron, A. Collier; Marsden, S. C.; Jardine, M.; Barnes, J.R.; Vlex, J. C. Ramirez; Donati, J. -F.

    2008-01-01

    We present the first measurements of surface differential rotation on a pre-main sequence binary system. Using intensity (Stokes I) and circularly polarised (Stokes V) timeseries spectra, taken over eleven nights at the Anglo-Australian Telescope (AAT), we incorporate a solar-like differential rotation law into the surface imaging process. We find that both components of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) binary system show significant differential rotation. The equator-pole...

  6. Evidence of accretion triggered oscillations in the pre-main-sequence interacting binary AK Sco

    CERN Document Server

    de Castro, Ana I Gomez; Talavera, Antonio

    2012-01-01

    Pre-main sequence (PMS) binaries are surrounded by circumbinary disks from which matter falls onto both components. The material dragged from the circumbinary disk flows onto each star through independent streams channelled by the variable gravitational field. The action of the bar-like potential is most prominent in high eccentricity systems made of two equal mass stars. AK Sco is a unique PMS system composed of two F5 stars in an orbit with e=0.47. Henceforth, it is an ideal laboratory to study matter infall in binaries and its role in orbit circularization. In this letter, we report the detection of a 1.3mHz ultra low frequency oscillation in the ultraviolet light curve at periastron passage. This oscillation last 7 ks being most likely fed by the gravitational energy released when the streams tails spiralling onto each star get in contact at periastron passage enhancing the accretion flow; this unveils a new mechanism for angular momentum loss during pre-main sequence evolution and a new type of interacti...

  7. An Unusual Eclipse of a Pre-Main Sequence Star in IC 348

    CERN Document Server

    Cohen, R E; Williams, E C

    2003-01-01

    A solar-like pre-main sequence star (TJ 108 = H 187 = LRLL 35 = HMW 15) in the extremely young cluster IC 348 has been found, which apparently experienced an eclipse lasting ~3.5 years, much longer than has ever been detected for any normal eclipsing binary. The light curve is flat-bottomed and rather symmetric, with a depth of 0.66 mag in Cousins I. During eclipse, the system reddened by \\~0.17 mag in R-I. We argue that the eclipsing body is not a star because of the small probability of detecting an eclipse in what would be a very widely separated binary. Instead, it appears that the eclipse was caused by a circumstellar or circumbinary cloud or disk feature which occulted the star, or one of its components, if it is a binary system. We emphasize the importance of more detailed study of this object, which appears to be a new member of a small class of pre-main sequence stars whose variability can be firmly linked to occultation by circumstellar (or circumbinary) matter.

  8. Pre-main sequence stars in the stellar association N11 in the Large Magellanic Cloud

    CERN Document Server

    Vallenari, Antonella; Sordo, Rosanna

    2009-01-01

    Magellanic Clouds are of extreme importance to the study of the star formation process in low metallicity environments. In this paper we report on the discovery of pre-main sequence candidates and young embedded stellar objects in N11 located in the Large Magellanic Cloud to cast light on the star formation scenario. We would like to remind that this comparison is complicated by the presence of a large age dispersion detected in the fields. Deep archive HST/ACS photometry is used to derive color-magnitude diagrams of the associations in N~11 and of the foreground field population. These data are complemented by archive IR Spitzer data which allow the detection of young embedded stellar objects. The spatial distribution of the pre-main sequence candidates and young embedded stellar objects is compared with literature data observed at different wavelengths, such as H$_{\\alpha}$ and CO maps, and with the distribution of OB and Herbig Ae/Be stars. The degree of clustering is derived using the Minimal Spanning Tre...

  9. Gaia-ESO Survey: The analysis of pre-main sequence stellar spectra

    CERN Document Server

    Lanzafame, A C; Damiani, F; Franciosini, E; Cottaar, M; Sousa, S G; Tabernero, H M; Klutsch, A; Spina, L; Biazzo, K; Prisinzano, L; Sacco, G G; Randich, S; Brugaletta, E; Mena, E Delgado; Adibekyan, V; Montes, D; Bonito, R; Gameiro, J F; Alcalá, J M; Hernández, J I González; Jeffries, R; Messina, S; Meyer, M; Gilmore, G; Asplund, M; Binney, J; Bonifacio, P; Drew, J E; Feltzing, S; Ferguson, A M N; Micela, G; Negueruela, I; Prusti, T; Rix, H-W; Vallenari, A; Alfaro, E J; Prieto, C Allende; Babusiaux, C; Bensby, T; Blomme, R; Bragaglia, A; Flaccomio, E; Francois, P; Hambly, N; Irwin, M; Koposov, S E; Korn, A J; Smiljanic, R; Van Eck, S; Walton, N; Bayo, A; Bergemann, M; Carraro, G; Costado, M T; Edvardsson, B; Heiter, U; Hill, V; Hourihane, A; Jackson, R J; Jofré, P; Lardo, C; Lewis, J; Lind, K; Magrini, L; Marconi, G; Martayan, C; Masseron, T; Monaco, L; Morbidelli, L; Sbordone, L; Worley, C C; Zaggia, S

    2015-01-01

    This paper describes the analysis of UVES and GIRAFFE spectra acquired by the Gaia-ESO Public Spectroscopic Survey in the fields of young clusters whose population includes pre-main sequence (PMS) stars. Both methods that have been extensively used in the past and new ones developed in the contest of the Gaia-ESO survey enterprise are available and used. The internal precision of these quantities is estimated by inter-comparing the results obtained by such different methods, while the accuracy is estimated by comparison with independent external data, like effective temperature and surface gravity derived from angular diameter measurements, on a sample of benchmarks stars. Specific strategies are implemented to deal with fast rotation, accretion signatures, chromospheric activity, and veiling. The analysis carried out on spectra acquired in young clusters' fields during the first 18 months of observations, up to June 2013, is presented in preparation of the first release of advanced data products. Stellar par...

  10. Theoretical study of $\\gamma$ Doradus pulsations in pre-main sequence stars

    CERN Document Server

    Bouabid, M -P; Miglio, A; Dupret, M -A; Grigahcène, A; Noels, A

    2010-01-01

    The question of the existence of pre-main sequence (PMS) $\\gamma$~Doradus ($\\gamma$~Dor) has been raised by the observations of young clusters such as NGC~884 hosting $\\gamma$~Dor members. We have explored the properties of $\\gamma$~Dor type pulsations in a grid of PMS models covering the mass range $1.2 M_\\odot < M_* < 2.5 M_\\odot$ and we derive the theoretical instability strip (IS) for the PMS $\\gamma$~Dor pulsators. We explore the possibility of distinguishing between PMS and MS $\\gamma$~Dor by the behaviour of the period spacing of their high order $gravity$-modes ($g$-modes).

  11. KH 15D: Gradual Occultation of a Pre-Main-Sequence Binary

    CERN Document Server

    Winn, J N; Johnson, J A; Stanek, K Z; Garnavich, P M; Winn, Joshua N.; Holman, Matthew J.; Johnson, John A.; Stanek, Krzysztof Z.; Garnavich, Peter M.

    2004-01-01

    We propose that the extraordinary "winking star" KH 15D is an eccentric pre-main-sequence binary that is gradually being occulted by an opaque screen. This model accounts for the periodicity, depth, duration, and rate of growth of the modern eclipses; the historical light curve from photographic plates; and the existing radial velocity measurements. It also explains the re-brightening events that were previously observed during mid-eclipse, and the subsequent disappearance of these events. We predict the future evolution of the system and its full radial velocity curve. Given the small velocity of the occulting screen relative to the center of mass of the binary, the screen is probably associated with the binary, and may be the edge of a precessing circumbinary disk.

  12. New radio detections of early-type pre-main-sequence stars

    Science.gov (United States)

    Skinner, Stephen L.; Brown, Alexander; Linsky, Jeffrey L.

    1990-01-01

    Results of VLA radio continuum observations of 13 early-type pre-main-sequence stars selected from the 1984 catalog of Finkenzeller and Mundt are presented. The stars HD 259431 and MWC 1080 were detected at 3.6 cm, while HD 200775 and TY CrA were detected at both 3.6 and 6 cm. The flux density of HD 200775 has a frequency dependence consistent with the behavior expected for free-free emission originating in a fully ionized wind. However, an observation in A configuration suggests that the source geometry may not be spherically symmetric. In contrast, the spectral index of TY CrA is negative with a flux behavior implying nonthermal emission. The physical mechanism responsible for the nonthermal emission has not yet been identified, although gyrosynchrotron and synchrotron processes cannot be ruled out.

  13. The magnetic field of the pre-main sequence Herbig Ae star HD 190073

    Science.gov (United States)

    Catala, C.; Alecian, E.; Donati, J.-F.; Wade, G. A.; Landstreet, J. D.; Böhm, T.; Bouret, J.-C.; Bagnulo, S.; Folsom, C.; Silvester, J.

    2007-01-01

    Context: The general context of this paper is the study of magnetic fields in the pre-main sequence intermediate mass Herbig Ae/Be stars. Magnetic fields are likely to play an important role in pre-main sequence evolution at these masses, in particular in controlling the gains and losses of stellar angular momentum. Aims: The particular aim of this paper is to announce the detection of a structured magnetic field in the Herbig Ae star HD 190073, and to discuss various scenarii for the geometry of the star, its environment and its magnetic field. Methods: We have used the ESPaDOnS spectropolarimeter at CFHT in 2005 and 2006 to obtain high-resolution, high signal-to-noise circular polarization spectra which demonstrate unambiguously the presence of a magnetic field in the photosphere of this star. Results: Nine circular polarization spectra were obtained, each one showing a clear Zeeman signature. This signature is suggestive of a magnetic field structured on large scales. The signature, which corresponds to a longitudinal magnetic field of 74± 10 G, does not vary detectably on a one-year timeframe, indicating either an azimuthally symmetric field, a zero inclination angle between the rotation axis and the line of sight, or a very long rotation period. The optical spectrum of HD 190073 exhibits a large number of emission lines. We discuss the formation of these emission lines in the framework of a model involving a turbulent heated region at the base of the stellar wind, possibly powered by magnetic accretion. Conclusions: .This magnetic detection contributes an important new observational discovery which will aid our understanding of stellar magnetism at intermediate masses. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

  14. Pre-main-sequence isochrones -- II. Revising star and planet formation timescales

    CERN Document Server

    Bell, Cameron P M; Mayne, N J; Jeffries, R D; Littlefair, S P

    2013-01-01

    We have derived ages for 13 young (<30 Myr) star-forming regions and find they are up to a factor two older than the ages typically adopted in the literature. This result has wide-ranging implications, including that circumstellar discs survive longer (~10-12 Myr) and that the average Class I lifetime is greater (~1 Myr) than currently believed. For each star-forming region we derived two ages from colour-magnitude diagrams. First we fitted models of the evolution between the zero-age main-sequence and terminal-age main-sequence to derive a homogeneous set of main-sequence ages, distances and reddenings with statistically meaningful uncertainties. Our second age for each star-forming region was derived by fitting pre-main-sequence stars to new semi-empirical model isochrones. For the first time (for a set of clusters younger than 50 Myr) we find broad agreement between these two ages, and since these are derived from two distinct mass regimes that rely on different aspects of stellar physics, it gives us c...

  15. Differential rotation on both components of the pre main-sequence binary system HD 155555

    CERN Document Server

    Dunstone, N J; Cameron, A Collier; Marsden, S C; Jardine, M; Barnes, J R; Vlex, J C Ramirez; Donati, J -F

    2008-01-01

    We present the first measurements of surface differential rotation on a pre-main sequence binary system. Using intensity (Stokes I) and circularly polarised (Stokes V) timeseries spectra, taken over eleven nights at the Anglo-Australian Telescope (AAT), we incorporate a solar-like differential rotation law into the surface imaging process. We find that both components of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) binary system show significant differential rotation. The equator-pole laptimes as determined from the intensity spectra are 80 days for the primary star and 163 days for the secondary. Similarly for the magnetic spectra we obtain equator-pole laptimes of 44 and 71 days respectively, showing that the shearing timescale of magnetic regions is approximately half that found for stellar spots. Both components are therefore found to have rates of differential rotation similar to those of the same spectral type main sequence single stars. The results for HD 155555 are therefore in contrast to tho...

  16. Pre-main-sequence isochrones -- III. The Cluster Collaboration isochrone server

    CERN Document Server

    Bell, Cameron P M; Naylor, Tim; Mayne, N J; Jeffries, R D; Mamajek, Eric E; Rowe, John

    2014-01-01

    We present an isochrone server for semi-empirical pre-main-sequence model isochrones in the following systems: Johnson-Cousins, Sloan Digital Sky Survey, Two-Micron All-Sky Survey, Isaac Newton Telescope (INT) Wide-Field Camera, and INT Photometric H$\\alpha$ Survey (IPHAS)/UV-Excess Survey (UVEX). The server can be accessed via the Cluster Collaboration webpage {http://www.astro.ex.ac.uk/people/timn/isochrones/}. To achieve this we have used the observed colours of member stars in young clusters with well-established age, distance and reddening to create fiducial loci in the colour-magnitude diagram. These empirical sequences have been used to quantify the discrepancy between the models and data arising from uncertainties in both the interior and atmospheric models, resulting in tables of semi-empirical bolometric corrections (BCs) in the various photometric systems. The model isochrones made available through the server are based on existing stellar interior models coupled with our newly derived semi-empiric...

  17. Pulsating pre-main sequence stars in IC 4996 and NGC 6530

    CERN Document Server

    Zwintz, K; Zwintz, Konstanze; Weiss, Werner W.

    2006-01-01

    Asteroseismology of pulsating pre-main sequence (PMS) stars has the potential of testing the validity of current models of PMS structure and evolution. As a first step, a sufficiently large sample of pulsating PMS stars has to be established, which allows to select candidates optimally suited for a detailed asteroseismological analysis based on photometry from space or ground based network data. A search for pulsating PMS members in the young open clusters IC 4996 and NGC 6530 has been performed to improve the sample of known PMS pulsators. As both clusters are younger than 10 million years, all members with spectral types later than A0 have not reached the zero-age main sequence yet. Hence, IC 4996 and NGC 6530 are most suitable to search for PMS pulsation among their A- and F-type cluster stars. CCD time series photometry in Johnson B and V filters has been obtained for IC 4996 and NGC 6530. The resulting light curves for 113 stars in IC 4996 and 194 stars in NGC 6530 have been subject to detailed frequency...

  18. Magnetic Activity of Pre-main Sequence Stars near the Stellar-Substellar Boundary

    CERN Document Server

    Principe, David A; Rodriguez, David

    2015-01-01

    X-ray observations of pre-main sequence (pre-MS) stars of M-type probe coronal emission and offer a means to investigate magnetic activity at the stellar-substellar boundary. Recent observations of main sequence (MS) stars at this boundary display a decrease in fractional X-ray luminosity ($L_{X}$/$L_{bol}$) by almost two orders of magnitude for spectral types M7 and later. We investigate magnetic activity and search for a decrease in X-ray emission in the pre-MS progenitors of these MS stars. We present XMM-Newton X-ray observations and preliminary results for ~10 nearby (30-70 pc), very low mass pre-MS stars in the relatively unexplored age range of 10-30 Myr. We compare the fractional X-ray luminosities of these 10-30 Myr old stars to younger (1-3 Myr) pre-MS brown dwarfs and find no dependence on spectral type or age suggesting that X-ray activity declines at an age later than ~30 Myr in these very low-mass stars.

  19. Magnetic Activity of Pre-main Sequence Stars near the Stellar-Substellar Boundary

    Science.gov (United States)

    Principe, David; Kastner, Joel. H.; Rodriguez, David

    2016-01-01

    X-ray observations of pre-main sequence (pre-MS) stars of M-type probe coronal emission and offer a means to investigate magnetic activity at the stellar-substellar boundary. Recent observations of main sequence (MS) stars at this boundary display a decrease in fractional X-ray luminosity (L X /L bol ) by almost two orders of magnitude for spectral types M7 and later. We investigate magnetic activity and search for a decrease in X-ray emission in the pre-MS progenitors of these MS stars. We present XMM-Newton X-ray observations and preliminary results for ~10 nearby (30-70 pc), very low mass pre-MS stars in the relatively unexplored age range of 10-30 Myr. We compare the fractional X-ray luminosities of these 10-30 Myr old stars to younger (1-3 Myr) pre-MS brown dwarfs and find no dependence on spectral type or age suggesting that X-ray activity declines at an age later than ~30 Myr in these very low-mass stars.

  20. The effect of starspots on the radii of low-mass pre-main sequence stars

    CERN Document Server

    Jackson, R J

    2014-01-01

    A polytropic model is used to investigate the effects of dark photospheric spots on the evolution and radii of magnetically active, low-mass (M<0.5Msun), pre-main sequence (PMS) stars. Spots slow the contraction along Hayashi tracks and inflate the radii of PMS stars by a factor of (1-beta)^{-N} compared to unspotted stars of the same luminosity, where beta is the equivalent covering fraction of dark starspots and N \\simeq 0.45+/-0.05. This is a much stronger inflation than predicted by the models of Spruit & Weiss (1986) for main sequence stars with the same beta, where N \\sim 0.2 to 0.3. These models have been compared to radii determined for very magnetically active K- and M-dwarfs in the young Pleiades and NGC 2516 clusters, and the radii of tidally-locked, low-mass eclipsing binary components. The binary components and ZAMS K-dwarfs have radii inflated by \\sim 10 per cent compared to an empirical radius-luminosity relation that is defined by magnetically inactive field dwarfs with interferometrica...

  1. Pre-main-sequence binaries with tidally disrupted discs: the Br gamma in HD 104237

    CERN Document Server

    Garcia, P J V; Dougados, C; Bacciotti, F; Clausse, J -M; Massi, F; Mérand, A; Petrov, R; Weigelt, G

    2013-01-01

    Active pre-main-sequence binaries with separations of around ten stellar radii present a wealth of phenomena unobserved in common systems. The study of these objects is extended from Classical T Tauri stars to the Herbig Ae star HD 104237. Spectro-interferometry with the VLTI/AMBER is presented. It is found that the K-band continuum squared visibilities are compatible with a circumbinary disc with a radius of ~0.5 AU. However, a significant fraction (~50 per cent) of the flux is unresolved and not fully accounted by the stellar photospheres. The stars probably don't hold circumstellar discs, in addition to the circumbinary disk, due to the combined effects of inner magnetospheric truncation and outer tidal truncation. This unresolved flux likely arises in compact structures inside the tidally disrupted circumbinary disc. Most ($\\gtrsim 90$ per cent) of the Br gamma line emission is unresolved. The line-to-continuum spectro-astrometry shifts in time, along the direction of the Ly alpha jet known to be driven b...

  2. The first magnetic maps of a pre-main sequence binary star system - HD 155555

    CERN Document Server

    Dunstone, N J; Cameron, A Collier; Marsden, S C; Jardine, M; Stempels, H C; Vlex, J C Ramirez; Donati, J -F

    2008-01-01

    We present the first maps of the surface magnetic fields of a pre-main sequence binary system. Spectropolarimetric observations of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) system were obtained at the Anglo-Australian Telescope in 2004 and 2007. Both datasets are analysed using a new binary Zeeman Doppler imaging (ZDI) code. This allows us to simultaneously model the contribution of each component to the observed circularly polarised spectra. Stellar brightness maps are also produced for HD 155555 and compared to previous Doppler images. Our radial magnetic maps reveal a complex surface magnetic topology with mixed polarities at all latitudes. We find rings of azimuthal field on both stars, most of which are found to be non-axisymmetric with the stellar rotational axis. We also examine the field strength and the relative fraction of magnetic energy stored in the radial and azimuthal field components at both epochs. A marked weakening of the field strength of the secondary star is observed between t...

  3. Exploring pre-main sequence variables of ONC: The new variables

    CERN Document Server

    Parihar, Padmakar; Distefano, Elisa; Shantikumar N S; Medhi, Biman J

    2009-01-01

    Since 2004, we have been engaged in a long-term observing program to monitor young stellar objects in the Orion Nebula Cluster. We have collected about two thousands frames in V, R, and I broad-band filters on more than two hundred nights distributed over five consecutive observing seasons. The high-quality and time-extended photometric data give us an opportunity to address various phenomena associated with young stars. The prime motivations of this project are i) to explore various manifestations of stellar magnetic activity in very young low-mass stars; ii) to search for new pre-main sequence eclipsing binaries; and iii) to look for any EXor and FUor like transient activities associated with YSOs. Since this is the first paper on this program, we give a detailed description of the science drivers, the observation and the data reduction strategies as well. In addition to these, we also present a large number of new periodic variables detected from our first five years of time-series photometric data. Our st...

  4. V4046 Sgr: Touchstone to Investigate Spectral Type Discrepancies for Pre-main Sequence Stars

    CERN Document Server

    Kastner, Joel H; Sargent, Benjamin; Smith, C T; Rayner, John

    2014-01-01

    Determinations of the fundamental properties (e.g., masses and ages) of late-type, pre-main sequence (pre-MS) stars are complicated by the potential for significant discrepancies between the spectral types of such stars as ascertained via optical vs. near-infrared observations. To address this problem, we have obtained near-IR spectroscopy of the nearby, close binary T Tauri system V4046 Sgr AB with the NASA Infrared Telescope Facility (IRTF) SPEX spectrometer. The V4046 Sgr close binary (and circumbinary disk) system provides an important test case for spectral type determination thanks to the stringent observational constraints on its component stellar masses (i.e., ~0.9 Msun each) as well as on its age (12-21 Myr) and distance (73 pc). Analysis of the IRTF data indicates that the composite near-IR spectral type for V4046 Sgr AB lies in the range M0-M1, i.e., significantly later than the K5+K7 composite type previously determined from optical spectroscopy. However, the K5+K7 composite type is in better agre...

  5. Hunting for millimeter flares from magnetic reconnection in pre-main sequence spectroscopic binaries

    CERN Document Server

    Kóspál, Á; Hogerheijde, M R; Moór, A; Blake, G A

    2010-01-01

    Recent observations of the low-mass pre-main sequence, eccentric spectroscopic binaries DQ Tau and V773 Tau A reveal that their millimeter spectrum is occasionally dominated by flares from non-thermal emission processes. The transient activity is believed to be synchrotron in nature, resulting from powerful magnetic reconnection events when the separate magnetic structures of the binary components are capable of interacting and forced to reorganize, typically near periastron. We conducted the first systematic study of the millimeter variability toward a sample of 12 PMS spectroscopic binaries with the aim to characterize the proliferation of flares amongst sources likely to experience similar interbinary reconnection events. The source sample consists of short-period, close-separation binaries that possess either a high orbital eccentricity or a circular orbit. Using the MAMBO2 array on the IRAM 30m telescope, we carried out continuous monitoring at 1.25 mm over a 4-night period during which all of the high-e...

  6. Tracing the potential planet-forming regions around seven pre-main-sequence stars

    CERN Document Server

    Schegerer, A A; Hummel, C A; Quanz, S P; Richichi, A

    2009-01-01

    We investigate the nature of the innermost regions of seven circumstellar disks around pre-main-sequence stars. Our object sample contains disks apparently at various stages of their evolution. Both single stars and spatially resolved binaries are considered. In particular, we search for inner disk gaps as proposed for several young stellar objects. When analyzing the underlying dust population in the atmosphere of circumstellar disks, the shape of the 10um feature is investigated. We performed interferometric observations in N band 8-13um with MIDI using baseline lengths of between 54m and 127m. The data analysis is based on radiative-transfer simulations using the Monte Carlo code MC3D by modeling simultaneously the SED, N band spectra, and interferometric visibilities. Correlated and uncorrelated N band spectra are compared to investigate the radial distribution of the dust composition of the disk atmosphere. Spatially resolved mid-infrared emission was detected in all objects. For four objects, the observ...

  7. RX J0942.7-7726AB: an isolated pre-main sequence wide binary

    CERN Document Server

    Murphy, Simon J; Bessell, Michael S

    2012-01-01

    We report the discovery of two young M-dwarfs, RX J0942.7-7726 (M1) and 2MASS J09424157-7727130 (M4.5), that were found only 42 arcsec apart in a survey for pre-main sequence stars surrounding the open cluster eta Chamaeleontis. Both stars have congruent proper motions and near-infrared photometry. Medium-resolution spectroscopy reveals that they are coeval (age 8-12 Myr), codistant (100-150 pc) and thus almost certainly form a true wide binary with a projected separation of 4000-6000 AU. The system appears too old and dynamically fragile to have originated in eta Cha and a traceback analysis argues for its birth in or near the Scorpius-Centaurus OB Association. RX J0942.7-7726AB joins a growing group of wide binaries kinematically linked to Sco-Cen, suggesting that such fragile systems can survive the turbulent environment of their natal molecular clouds while still being dispersed with large velocities. Conversely, the small radial velocity difference between the stars (2.7 \\pm 1.0 km/s) could mean the syst...

  8. The quadruple pre-main sequence system LkCa3: Implications for stellar evolution models

    CERN Document Server

    Torres, Guillermo; Badenas, Mariona; Prato, L; Schaefer, G H; Wasserman, Lawrence H; Mathieu, Robert D; Latham, David W

    2013-01-01

    We report the discovery that the pre-main sequence object LkCa3 in the Taurus-Auriga star-forming region is a hierarchical quadruple system of M stars. It was previously known to be a close (~0.5 arc sec) visual pair, with one component being a moderately eccentric 12.94-day single-lined spectroscopic binary. A re-analysis of archival optical spectra complemented with new near-infrared spectroscopy shows both visual components to be double-lined, the second one having a period of 4.06 days and a circular orbit. In addition to the orbital elements, we determine optical and near-infrared flux ratios, effective temperatures, and projected rotational velocities for all four stars. Using existing photometric monitoring observations of the system that had previously revealed the rotational period of the primary in the longer-period binary, we detect also the rotational signal of the primary in the 4.06-day binary, which is synchronized with the orbital motion. With only the assumption of coevality, a comparison of ...

  9. Older and Colder: The impact of starspots on pre-main sequence stellar evolution

    CERN Document Server

    Somers, Garrett

    2015-01-01

    We assess the impact of starspots on the evolution of late-type stars during the pre-main sequence (pre-MS) using a modified stellar evolution code. We find that heavily spotted models of mass 0.1-1.2\\msun\\ are inflated by up to $10$% during the pre-MS, and up to 4% and 9% for fully- and partially-convective stars at the zero-age MS, consistent with measurements from active eclipsing binary systems. Spots similarly decrease stellar luminosity and $T_{\\rm eff}$, causing isochrone-derived masses to be under-estimated by up to a factor of $2 \\times$, and ages to be under-estimated by a factor of 2-10$\\times$, at 3 Myr. Consequently, pre-MS clusters and their active stars are systematically older and more massive than often reported. Cluster ages derived with the lithium depletion boundary technique are erroneously young by $\\sim 15$% and $10$% at $30$ and $100$ Myr respectively, if 50% spotted stars are interpreted with un-spotted models. Finally, lithium depletion is suppressed in spotted stars with radiative c...

  10. Deep near-IR variability survey of pre-main-sequence stars in Rho Ophiuchi

    CERN Document Server

    de Oliveira, Catarina Alves

    2008-01-01

    Variability is a common characteristic of pre-main-sequence stars (PMS). Near-IR variability surveys of young stellar objects (YSOs) can probe stellar and circumstellar environments and provide information about the dynamics of the on going magnetic and accretion processes. Furthermore, variability can be used as a tool to uncover new cluster members in star formation regions. We hope to achieve the deepest near-IR variability study of YSOs targeting the Rho Ophiuchi cluster. Fourteen epochs of observations were obtained with the Wide Field Camera (WFCAM) at the UKIRT telescope scheduled in a manner that allowed the study of variability on timescales of days, months, and years. Statistical tools, such as the multi-band cross correlation index and the reduced chi-square, were used to disentangle signals of variability from noise. Variability characteristics are compared to existing models of YSOs in order to relate them to physical processes, and then used to select new candidate members of this star-forming r...

  11. The Recurrent Eclipse of an Unusual Pre--Main-Sequence Star in IC 348

    CERN Document Server

    Nordhagen, S; Williams, E C; Semkov, E

    2006-01-01

    The recurrence of a previously documented eclipse of a solar-like pre--main-sequence star in the young cluster IC 348 has been observed. The recurrence interval is 4.7 $\\pm 0.1$ yr and portions of 4 cycles have now been seen. The duration of each eclipse is at least 3.5 years, or $\\sim 75$% of a cycle, verifying that this is not an eclipse by a stellar companion. The light curve is generally symmetric and approximately flat-bottomed. Brightness at maximum and minimum have been rather stable over the years but the light curve is not perfectly repetitive or smooth and small variations exist at all phases. We confirm that the star is redder when fainter. Models are discussed and it is proposed that this could be a system similar to KH 15D in NGC 2264. Specifically, it may be an eccentric binary in which a portion of the orbit of one member is currently occulted during some binary phases by a circumbinary disk. The star deserves sustained observational attention for what it may reveal about the circumstellar envi...

  12. Fundamental properties of pre-main sequence stars in young, southern star forming regions: metallicities

    CERN Document Server

    James, D J; Santos, N C; Bouvier, J; James, David J.; Melo, Claudio; Santos, Nuno C.; Bouvier, Jerome

    2005-01-01

    Aims: The primary motivation for this project is to search for metal-rich star forming regions, in which, stars of super-solar metallicity will be created, as hopefully, will be extra-solar planets orbiting them ! Results: We find (pre-main sequence) model-dependent isochronal ages of the Lupus, Chamaeleon and CrA targets to be $9.1 \\pm 2.1$ Myr, $4.5 \\pm 1.6$ Myr and $9.0 \\pm 3.9$ Myr respectively. The majority of the stars have Li I 6707.8A equivalent widths similar to, or above those of, their similar mass Pleiades counterparts, confirming their youthfulness. Most stars are kinematic members, either single or binary, of their regions. We find a mean radial velocity for objects in the Lupus cloud to be ${\\bar {RV}}=+2.6 \\pm 1.8$ km s$^{-1}$, for the Chamaeleon I & II clouds, ${\\bar {RV}}=+12.8 \\pm 3.6$ km s$^{-1}$ whereas for the CrA cloud, we find ${\\bar {RV}}=-1.1 \\pm 0.5$ km s$^{-1}$. All stars are coronally and chromospherically active, exhibiting X-ray and H$\\alpha$ emission levels marginally less,...

  13. Pre-main sequence stars older than 8 Myr in the Eagle Nebula

    CERN Document Server

    De Marchi, Guido; Guarcello, M G; Bonito, Rosaria

    2013-01-01

    Attention is given to a population of 110 stars in the NGC 6611 cluster of the Eagle Nebula that have prominent near-infrared (NIR) excess and optical colours typical of pre-main sequence (PMS) stars older than 8 Myr. At least half of those for which spectroscopy exists have a Halpha emission line profile revealing active accretion. In principle, the V-I colours of all these stars would be consistent with those of young PMS objects (< 1 Myr) whose radiation is heavily obscured by a circumstellar disc seen at high inclination and in small part scattered towards the observer by the back side of the disc. However, using theoretical models it is shown here that objects of this type can only account for a few percent of this population. In fact, the spatial distribution of these objects, their X-ray luminosities, their optical brightness, their positions in the colour-magnitude diagram and the weak Li absorption lines of the stars studied spectroscopically suggest that most of them are at least 8 times older th...

  14. An extensive VLT/X-shooter library of photospheric templates of pre-main sequence stars

    Science.gov (United States)

    Manara, C. F.; Frasca, A.; Alcalá, J. M.; Natta, A.; Stelzer, B.; Testi, L.

    2017-09-01

    Context. Studies of the formation and evolution of young stars and their disks rely on knowledge of the stellar parameters of the young stars. The derivation of these parameters is commonly based on comparison with photospheric template spectra. Furthermore, chromospheric emission in young active stars impacts the measurement of mass accretion rates, a key quantity for studying disk evolution. Aims: Here we derive stellar properties of low-mass (M⋆≲ 2 M⊙) pre-main sequence stars without disks, which represent ideal photospheric templates for studies of young stars. We also use these spectra to constrain the impact of chromospheric emission on the measurements of mass accretion rates. The spectra are reduced, flux-calibrated, and corrected for telluric absorption, and are made available to the community. Methods: We derive the spectral type for our targets by analyzing the photospheric molecular features present in their VLT/X-shooter spectra by means of spectral indices and comparison of the relative strength of photospheric absorption features. We also measure effective temperature, gravity, projected rotational velocity, and radial velocity from our spectra by fitting them with synthetic spectra with the ROTFIT tool. The targets have negligible extinction (AVhttp://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/605/A86

  15. Constraints on the height of the inner disk rim in pre-main-sequence stars

    CERN Document Server

    Vinković, Dejan

    2014-01-01

    The structure of inner region of protoplanetary disks around young pre-main-sequence stars is still poorly understood. This part of the disk is shaped by various forces influencing dust and gas dynamics and by dust sublimation, which creates abrupt drops in the dust density. This region also emits a strong near-infrared excess that cannot be explained by classical accretion disk models, which suggests the existence of some unusual dust distribution or disk shape. The most prevalent explanation to date is the puffed-up inner disk rim model, where the disk exhibits an optically thin cavity around the star up to the distance of dust sublimation. The critical parameter in this model is the inner disk rim height $z_{\\rm max}$ relative to the rim's distance from the star $R_{\\rm in}$. Observations often require $z_{\\rm max}/R_{\\rm in}\\gtrsim0.2$ to reproduce the near-infrared excess in the spectra. In this paper we put together a comprehensive list of processes that can shape the inner disk rim and combined them to...

  16. Exploring pre-main-sequence variables of the ONC: the new variables

    Science.gov (United States)

    Parihar, Padmakar; Messina, Sergio; Distefano, Elisa; Shantikumar, N. S.; Medhi, Biman J.

    2009-12-01

    Since 2004, we have been engaged in a long-term observing programme to monitor young stellar objects (YSOs) in the Orion Nebula Cluster (ONC). We have collected about 2000 frames in V, R and I broad-band filters on more than 200 nights distributed over five consecutive observing seasons. The high-quality and time-extended photometric data give us an opportunity to address various phenomena associated with young stars. The prime motivations of this project are (i) to explore various manifestations of stellar magnetic activity in very young low-mass stars, (ii) to search for new pre-main-sequence eclipsing binaries and (iii) to look for any EXor and FUor-like transient activities associated with YSOs. Since this is the first paper on this programme, we give a detailed description of the science drivers, the observation and the data reduction strategies as well. In addition to these, we also present a large number of new periodic variables detected from our first 5 yr of time-series photometric data. Our study reveals that about 72 per cent of classical T Tauri stars (CTTS) in our field of view are periodic, whereas only 32 per cent of weak-lined T Tauri stars (WTTS) are periodic. This indicates that inhomogeneity patterns on the surface of CTTS of the ONC stars are much more stable than on WTTS. From our multiyear monitoring campaign, we found that the photometric surveys based on single season are incapable of identifying all periodic variables. And any study on evolution of angular momentum based on single-season surveys must be carried out with caution.

  17. YSOVAR: SIX PRE-MAIN-SEQUENCE ECLIPSING BINARIES IN THE ORION NEBULA CLUSTER

    Energy Technology Data Exchange (ETDEWEB)

    Morales-Calderon, M.; Stauffer, J. R.; Rebull, L. M. [Spitzer Science Center, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125 (United States); Stassun, K. G. [Physics and Astronomy Department, Vanderbilt University, 1807 Station B, Nashville, TN 37235 (United States); Vrba, F. J. [U. S. Naval Observatory, Flagstaff Station, 10391 W. Naval Observatory Road, Flagstaff, AZ 86001-8521 (United States); Prato, L. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Hillenbrand, L. A.; Carpenter, J. M. [Astronomy Department, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125 (United States); Terebey, S.; Angione, J. [Department of Physics and Astronomy, California State University at Los Angeles, Los Angeles, CA 90032 (United States); Covey, K. R. [Department of Astronomy, Cornell University, 226 Space Sciences Building, Ithaca, NY 14853 (United States); Terndrup, D. M. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Gutermuth, R. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Song, I. [Physics and Astronomy Department, University of Georgia, Athens, GA 30602-2451 (United States); Plavchan, P. [NASA Exoplanet Science Institute, California Institute of Technology, Pasadena, CA 91125 (United States); Marchis, F. [SETI Institute, Carl Sagan Center, 189 N San Bernado Av, Mountain View, CA 94043 (United States); Garcia, E. V. [Department of Physics, Fisk University, 1000 17th Ave. N, Nashville, TN 37208 (United States); Margheim, S. [Gemini Observatory, Southern Operations Center, Casilla 603, La Serena (Chile); Luhman, K. L. [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States); Irwin, J. M., E-mail: mariamc@cab.inta-csic.es [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States)

    2012-07-10

    Eclipsing binaries (EBs) provide critical laboratories for empirically testing predictions of theoretical models of stellar structure and evolution. Pre-main-sequence (PMS) EBs are particularly valuable, both due to their rarity and the highly dynamic nature of PMS evolution, such that a dense grid of PMS EBs is required to properly calibrate theoretical PMS models. Analyzing multi-epoch, multi-color light curves for {approx}2400 candidate Orion Nebula Cluster (ONC) members from our Warm Spitzer Exploration Science Program YSOVAR, we have identified 12 stars whose light curves show eclipse features. Four of these 12 EBs are previously known. Supplementing our light curves with follow-up optical and near-infrared spectroscopy, we establish two of the candidates as likely field EBs lying behind the ONC. We confirm the remaining six candidate systems, however, as newly identified ONC PMS EBs. These systems increase the number of known PMS EBs by over 50% and include the highest mass ({theta}{sup 1} Ori E, for which we provide a complete set of well-determined parameters including component masses of 2.807 and 2.797 M{sub Sun }) and longest-period (ISOY J053505.71-052354.1, P {approx} 20 days) PMS EBs currently known. In two cases ({theta}{sup 1} Ori E and ISOY J053526.88-044730.7), enough photometric and spectroscopic data exist to attempt an orbit solution and derive the system parameters. For the remaining systems, we combine our data with literature information to provide a preliminary characterization sufficient to guide follow-up investigations of these rare, benchmark systems.

  18. THE QUADRUPLE PRE-MAIN-SEQUENCE SYSTEM LkCa 3: IMPLICATIONS FOR STELLAR EVOLUTION MODELS

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Guillermo; Latham, David W. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Ruiz-Rodriguez, Dary; Prato, L.; Wasserman, Lawrence H. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Badenas, Mariona [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Schaefer, G. H. [CHARA Array of Georgia State University, Mount Wilson Observatory, Mount Wilson, CA 91023 (United States); Mathieu, Robert D., E-mail: gtorres@cfa.harvard.edu [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-08-10

    We report the discovery that the pre-main-sequence (PMS) object LkCa 3 in the Taurus-Auriga star-forming region is a hierarchical quadruple system of M stars. It was previously known to be a close ({approx}0.''5) visual pair, with one component being a moderately eccentric 12.94 day single-lined spectroscopic binary. A re-analysis of archival optical spectra complemented by new near-infrared (NIR) spectroscopy shows both visual components to be double lined; the second one has a period of 4.06 days and a circular orbit. In addition to the orbital elements, we determine optical and NIR flux ratios, effective temperatures, and projected rotational velocities for all four stars. Using existing photometric monitoring observations of the system that had previously revealed the rotational period of the primary in the longer-period binary, we also detect the rotational signal of the primary in the 4.06 day binary, which is synchronized with the orbital motion. With only the assumption of coevality, a comparison of all of these constraints with current stellar evolution models from the Dartmouth series points to an age of 1.4 Myr and a distance of 133 pc, consistent with previous estimates for the region and suggesting that the system is on the near side of the Taurus complex. Similar comparisons of the properties of LkCa 3 and the well-known quadruple PMS system GG Tau with the widely used models from the Lyon series for a mixing length parameter of {alpha}{sub ML} = 1.0 strongly favor the Dartmouth models.

  19. X-ray Emission Properties of Intermediate-Mass, Pre-Main-Sequence Stars

    Science.gov (United States)

    Povich, Matthew S.; Binder, Breanna; Townsley, Leisa K.; Broos, Patrick S.

    2017-08-01

    Intermediate-mass (2-8 M⊙) main-sequence stars with A to mid-B spectral types occupy an X-ray "desert" of weak intrinsic emission between low- and high-mass stars. Lacking the wind-shock driven emission of massive, O and early B stars or the convectively-driven magnetic reconnection flaring activity of later-type stars, X-ray detections of (non-peculiar) main-sequence AB stars are typically ascribed to the presence of unresolved, lower-mass binary companions. There is mounting evidence, however, that intermediate-mass, pre-main sequence stars (IMPS) with GK spectral types produce intrinsic X-ray emission that rapidly decays with time following the development of a radiative zone as IMPS approach the ZAMS as AB stars. This suggests that X-ray emission from IMPS may be a more luminous analog of the well-studied coronal X-ray emission from lower-mass, T Tauri stars. Statistical studies of young IMPS have been hampered by their scarcety in nearby, unobscured star-forming regions. We present the first results from a spectral-fitting study to measure absorption-corrected X-ray luminosities and plasma temperatures for hundreds of candidate X-ray emitting IMPS found in the MYStIX and MAGiX surveys of massive Galactic star forming regions. Candidate IMPS are placed on the HR diagram via a novel infrared spectral energy distribution modeling technique designed for highly-obscured, young massive star-forming regions. The rapid decay of X-ray emission from these objects has the potential to provide an independent chronometer to constrain star formation rates, and may produce an age-dependent bias in the relationship between the stellar X-ray luminosity function and mass function in distant (>2 kpc) regions observed with relatively shallow X-ray observations.This work is supported by the National Science Foundation under grant CAREER-1454334 and by NASA through Chandra Award 18200040.

  20. Measuring the mass of a pre-main sequence binary star through the orbit of TWA5A

    Energy Technology Data Exchange (ETDEWEB)

    Konopacky, Q; Ghez, A; Duchene, G; McCabe, C; Macintosh, B

    2007-01-18

    We present the results of a five year monitoring campaign of the close binary TWA 5Aab in the TW Hydrae association, using speckle and adaptive optics on the W.M. Keck 10 m telescopes. These measurements were taken as part of our ongoing monitoring of pre-main sequence (PMS) binaries in an effort to increase the number of dynamically determined PMS masses and thereby calibrate the theoretical PMS evolutionary tracks. Our observations have allowed us to obtain the first determination of this system's astrometric orbit. We find an orbital period of 5.94 {+-} 0.09 years and a semi-major axis of 0.''066 {+-} 0.''005. Combining these results with a kinematic distance, we calculate a total mass of 0.71 {+-} 0.14 M{sub {circle_dot}} (D/44 pc){sup 3}. for this system. This mass measurement, as well as the estimated age of this system, are consistent to within 2{sigma} of all theoretical models considered. In this analysis, we properly account for correlated uncertainties, and show that while these correlations are generally ignored, they increase the formal uncertainties by up to a factor of five and therefore are important to incorporate. With only a few more years of observation, this type of measurement will allow the theoretical models to be distinguished.

  1. An Internet server for update pre-main sequence tracks of low- and intermediate-mass stars

    CERN Document Server

    Siess, L; Forestini, M

    2000-01-01

    We present new grids of pre-main sequence (PMS) tracks for stars in the mass range 0.1 to 7.0 Msun. The computations were performed for four different metallicities (Z=0.01, 0.02, 0.03 and 0.04). A fifth table has been computed for the solar composition (Z=0.02), including a moderate overshooting. We describe the update in the physics of the Grenoble stellar evolution code which concerns mostly changes in the equation of state (EOS) adopting the formalism proposed by Pols et al. (1995) and in the treatment of the boundary condition. Comparisons of our models with other grids demonstrate the validity of this EOS in the domain of very low-mass stars. Finally, we present a new server dedicated to PMS stellar evolution which allows the determination of stellar parameters from observational data, the calculation of isochrones, the retrieval of evolutionary files and the possibility to generate graphic outputs. WWW site : http://www-laog.obs.ujf-grenoble.fr/activites/starevol/evol.html

  2. Revisiting the pre-main-sequence evolution of stars. I. Importance of accretion efficiency and deuterium abundance

    Science.gov (United States)

    Kunitomo, Masanobu; Guillot, Tristan; Takeuchi, Taku; Ida, Shigeru

    2017-03-01

    Context. Protostars grow from the first formation of a small seed and subsequent accretion of material. Recent theoretical work has shown that the pre-main-sequence (PMS) evolution of stars is much more complex than previously envisioned. Instead of the traditional steady, one-dimensional solution, accretion may be episodic and not necessarily symmetrical, thereby affecting the energy deposited inside the star and its interior structure. Aims: Given this new framework, we want to understand what controls the evolution of accreting stars. Methods: We use the MESA stellar evolution code with various sets of conditions. In particular, we account for the (unknown) efficiency of accretion in burying gravitational energy into the protostar through a parameter, ξ, and we vary the amount of deuterium present. Results: We confirm the findings of previous works that, in terms of evolutionary tracks on an Hertzprung-Russell (H-R) diagram, the evolution changes significantly with the amount of energy that is lost during accretion. We find that deuterium burning also regulates the PMS evolution. In the low-entropy accretion scenario, the evolutionary tracks in the H-R diagram are significantly different from the classical tracks and are sensitive to the deuterium content. A comparison of theoretical evolutionary tracks and observations allows us to exclude some cold accretion models (ξ 0) with low deuterium abundances. Conclusions: We confirm that the luminosity spread seen in clusters can be explained by models with a somewhat inefficient injection of accretion heat. The resulting evolutionary tracks then become sensitive to the accretion heat efficiency, initial core entropy, and deuterium content. In this context, we predict that clusters with a higher D/H ratio should have less scatter in luminosity than clusters with a smaller D/H. Future work on this issue should include radiation-hydrodynamic simulations to determine the efficiency of accretion heating and further

  3. Hunting for millimeter flares from magnetic reconnection in pre-main sequence spectroscopic binaries

    Science.gov (United States)

    Kóspál, Á.; Salter, D. M.; Hogerheijde, M. R.; Moór, A.; Blake, G. A.

    2011-03-01

    Context. Recent observations of the low-mass pre-main sequence (PMS), eccentric spectroscopic binaries DQ Tau and V773 Tau A reveal that their millimeter spectrum is occasionally dominated by flares from non-thermal emission processes. The transient activity is believed to be synchrotron in nature, resulting from powerful magnetic reconnection events when the separate magnetic structures of the binary components are briefly capable of interacting and forced to reorganize, typically near periastron. Aims: We conducted the first systematic study of the millimeter variability toward a sample of 12 PMS spectroscopic binaries with the aim to characterize the proliferation of flares amongst sources likely to experience similar interbinary reconnection events. The source sample consists entirely of short-period, close-separation binaries that possess either a high orbital eccentricity (e > 0.1) or a circular orbit (e ≈ 0). Methods: Using the MAMBO2 array on the IRAM 30 m telescope, we carried out continuous monitoring at 1.25 mm (240 GHz) over a 4-night period during which all of the high-eccentricity binaries approached periastron. We also obtained simultaneous optical VRI measurements, since a strong link is often observed between stellar reconnection events (traced via X-rays) and optical brightenings. Results: UZ Tau E is the only source to be detected at millimeter wavelengths, and it exhibited significant variation (F1.25mm = 87-179 mJy); it is also the only source to undergo strong simultaneous optical variability (ΔR ≈ 0.9 mag). The binary possesses the largest orbital eccentricity in the current sample, a predicted factor in star-star magnetic interaction events. With orbital parameters and variable accretion activity similar to DQ Tau, the millimeter behavior of UZ Tau E draws many parallels to the DQ Tau model for colliding magnetospheres. However, on the basis of our observations alone, we cannot determine whether the variability is repetitive, or if it

  4. The Interior Structure Constants as an Age Diagnostic for Low-Mass, Pre-Main Sequence Detached Eclipsing Binary Stars

    CERN Document Server

    Feiden, Gregory A

    2013-01-01

    We propose a novel method for determining the ages of low-mass, pre-main sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5 -- 10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal,...

  5. Age-Related Observations of Low Mass Pre-Main and Young Main Sequence Stars (Invited Review)

    CERN Document Server

    Hillenbrand, Lynne A

    2008-01-01

    This overview summarizes the age dating methods available for young sub-solar mass stars. Pre-main sequence age diagnostics include the Hertzsprung-Russell (HR) diagram, spectroscopic surface gravity indicators, and lithium depletion; asteroseismology is also showing recent promise. Near and beyond the zero-age main sequence, rotation period or vsini and activity (coronal and chromospheric) diagnostics along with lithium depletion serve as age proxies. Other authors in this volume present more detail in each of the aforementioned areas. Herein, I focus on pre-main sequence HR diagrams and address the questions: Do empirical young cluster isochrones match theoretical isochrones? Do isochrones predict stellar ages consistent with those derived via other independent techniques? Do the observed apparent luminosity spreads at constant effective temperature correspond to true age spreads? While definitive answers to these questions are not provided, some methods of progression are outlined.

  6. A Critical Assessment of Ages Derived Using Pre-Main-Sequence Isochrones in Colour-Magnitude Diagrams

    Science.gov (United States)

    Bell, Cameron P. M.

    2012-11-01

    In this thesis a critical assessment of the ages derived using theoretical pre-main-sequence (pre-MS) stellar evolutionary models is presented by comparing the predictions to the low-mass pre-MS population of 14 young star-forming regions (SFRs) in colour-magnitude diagrams (CMDs). Deriving pre-MS ages requires precise distances and estimates of the reddening. Therefore, the main-sequence (MS) members of the SFRs have been used to derive a self-consistent set of statistically robust ages, distances and reddenings with associated uncertainties using a maximum-likelihood fitting statistic and MS evolutionary models. A photometric method for de-reddening individual stars - known as the Q-method - in regions where the extinction is spatially variable has been updated and is presented. The effects of both the model dependency and the SFR composition on these derived parameters are also discussed. The problem of calibrating photometric observations of red pre-MS stars is examined and it is shown that using observations of MS stars to transform the data into a standard photometric system can introduce significant errors in the position of the pre-MS locus in CMD space. Hence, it is crucial that precise photometric studies - especially of pre-MS objects - be carried out in the natural photometric system of the observations. This therefore requires a robust model of the system responses for the instrument used, and thus the calculated responses for the Wide-Field Camera on the Isaac Newton Telescope are presented. These system responses have been tested using standard star observations and have been shown to be a good representation of the photometric system. A benchmark test for the pre-MS evolutionary models is performed by comparing them to a set of well-calibrated CMDs of the Pleiades in the wavelength regime 0.4-2.5 μm. The masses predicted by these models are also tested against dynamical masses using a sample of MS binaries by calculating the system magnitude in a

  7. A Wide-Field Survey for Transiting Hot Jupiters and Eclipsing Pre-Main-Sequence Binaries in Young Stellar Associations

    CERN Document Server

    Oelkers, Ryan J; Marshall, Jennifer L; DePoy, Darren L; Lambas, Diego G; Colazo, Carlos; Stringer, Katelyn

    2016-01-01

    The past two decades have seen a significant advancement in the detection, classification and understanding of exoplanets and binaries. This is due, in large part, to the increase in use of small-aperture telescopes (< 20 cm) to survey large areas of the sky to milli-mag precision with rapid cadence. The vast majority of the planetary and binary systems studied to date consist of main-sequence or evolved objects, leading to a dearth of knowledge of properties at early times (< 50 Myr). Only a dozen binaries and one candidate transiting Hot Jupiter are known among pre-main sequence objects, yet these are the systems that can provide the best constraints on stellar formation and planetary migration models. The deficiency in the number of well-characterized systems is driven by the inherent and aperiodic variability found in pre-main-sequence objects, which can mask and mimic eclipse signals. Hence, a dramatic increase in the number of young systems with high-quality observations is highly desirable to gui...

  8. A statistical analysis of X-ray variability in pre-main sequence objects of the Taurus Molecular Cloud

    CERN Document Server

    Stelzer, B; Briggs, K; Micela, G; Scelsi, L; Audard, M; Pillitteri, I; Güdel, M

    2006-01-01

    This work is part of a systematic X-ray survey of the Taurus star forming complex with XMM-Newton. We study the time series of all X-ray sources associated with Taurus members, to statistically characterize their X-ray variability, and compare the results to those for pre-main sequence stars in the Orion Nebula Cluster and to expectations arising from a model where all the X-ray emission is the result of a large number of stochastically occurring flares. We find that roughly half of the detected X-ray sources show variability above our sensitivity limit, and in ~ 26 % of the cases this variability is recognized as flares. Variability is more frequently detected at hard than at soft energies. The variability statistics of cTTS and wTTS are undistinguishable, suggesting a common (coronal) origin for their X-ray emission. We have for the first time applied a rigorous maximum likelihood method in the analysis of the number distribution of flare energies on pre-main sequence stars. In its differential form this di...

  9. The Mdot - M* relation of pre-main sequence stars: a consequence of X-ray driven disc evolution

    CERN Document Server

    Ercolano, B; Owen, J E; Rosotti, G; Manara, C F

    2013-01-01

    We analyse current measurements of accretion rates onto pre-main sequence stars as a function of stellar mass, and conclude that the steep dependance of accretion rates on stellar mass is real and not driven by selection/detection threshold, as has been previously feared. These conclusions are reached by means of statistical tests including a survival analysis which can account for upper limits. The power-law slope of the Mdot-M* relation is found to be in the range of 1.6-1.9 for young stars with masses lower than 1 Msun. The measured slopes and distributions can be easily reproduced by means of a simple disc model which includes viscous accretion and X-ray photoevaporation. We conclude that the Mdot-M* relation in pre-main sequence stars bears the signature of disc dispersal by X-ray photoevaporation, suggesting that the relation is a straight- forward consequence of disc physics rather than an imprint of initial conditions.

  10. Pre-Main sequence Turn-On as a chronometer for young clusters: NGC346 as a benchmark

    CERN Document Server

    Cignoni, M; Sabbi, E; Nota, A; Degl'Innocenti, S; Moroni, P G Prada; Gallagher, J S

    2010-01-01

    We present a novel approach to derive the age of very young star clusters, by using the Turn-On (TOn). The TOn is the point in the color-magnitude diagram (CMD) where the pre-main sequence (PMS) joins the main sequence (MS). In the MS luminosity function (LF) of the cluster, the TOn is identified as a peak followed by a dip. We propose that by combining the CMD analysis with the monitoring of the spatial distribution of MS stars it is possible to reliably identify the TOn in extragalactic star forming regions. Compared to alternative methods, this technique is complementary to the turn-off dating and avoids the systematic biases affecting the PMS phase. We describe the method and its uncertainties, and apply it to the star forming region NGC346, which has been extensively imaged with the Hubble Space Telescope (HST). This study extends the LF approach in crowded extragalactic regions and opens the way for future studies with HST/WFC3, JWST and from the ground with adaptive optics.

  11. Pre-main sequence accretion in the low metallicity Galactic star-forming region Sh 2-284

    CERN Document Server

    Kalari, V M

    2014-01-01

    We present optical spectra of pre-main sequence (PMS) candidates around the H$\\alpha$ region taken with the Southern African Large Telescope, SALT, in the low metallicity ($Z$) Galactic region Sh 2-284, which includes the open cluster Dolidze 25 with an atypical low metallicity of $Z$ $\\sim$ 1/5 $Z_{\\odot}$. It has been suggested on the basis of both theory and observations that PMS mass-accretion rates, $\\dot M_{\\rm{acc}}$, are a function of $Z$. We present the first sample of spectroscopic estimates of mass-accretion rates for PMS stars in any low-$Z$ star-forming region. Our data-set was enlarged with literature data of H$\\alpha$ emission in intermediate-resolution R-band spectroscopy. Our total sample includes 24 objects spanning a mass range between 1 - 2 $M_{\\odot}$ and with a median age of approximately 3.5 Myr. The vast majority (21 out of 24) show evidence for a circumstellar disk on the basis of 2MASS and Spitzer infrared photometry. We find $\\dot M_{\\rm{acc}}$ in the 1 - 2 $M_{\\odot}$ interval to d...

  12. Impact of internal gravity waves on the rotation profile inside pre-main sequence low-mass stars

    CERN Document Server

    Charbonnel, C; Amard, L; Palacios, A; Talon, S

    2013-01-01

    We study the impact of internal gravity waves (IGW), meridional circulation, shear turbulence, and stellar contraction on the internal rotation profile and surface velocity evolution of solar metallicity low-mass pre-main sequence stars. We compute a grid of rotating stellar evolution models with masses between 0.6 and 2.0Msun taking these processes into account for the transport of angular momentum, as soon as the radiative core appears and assuming no more disk-locking from that moment on.IGW generation along the PMS is computed taking Reynolds-stress and buoyancy into account in the bulk of the stellar convective envelope and convective core (when present). Redistribution of angular momentum within the radiative layers accounts for damping of prograde and retrograde IGW by thermal diffusivity and viscosity in corotation resonance. Over the whole mass range considered, IGW are found to be efficiently generated by the convective envelope and to slow down the stellar core early on the PMS. In stars more massi...

  13. Magnetic fields and differential rotation on the pre-main sequence III: The early-G star HD 106506

    CERN Document Server

    Waite, I A; Carter, B D; Hart, R; Donati, J -F; Vélez, J C Ramírez; Semel, M; Dunstone, N

    2011-01-01

    We present photometry and spectropolarimetry of the pre-main sequence star HD 106506. A photometric rotational period of ~1.416 +/- 0.133 days has been derived using observations at Mount Kent Observatory (MKO). Spectropolarimetric data taken at the 3.9-m Anglo-Australian Telescope (AAT) were used to derive spot occupancy and magnetic maps of the star through the technique of Zeeman Doppler imaging (ZDI). The resulting brightness maps indicate that HD 106506 displays photospheric spots at all latitudes including a predominant polar spot. Azimuthal and radial magnetic images of this star have been derived, and a significant azimuthal magnetic field is indicated, in line with other active young stars. A solar-like differential rotation law was incorporated into the imaging process. Using Stokes I information the equatorial rotation rate, $\\Omega_{eq}$, was found to be 4.54 +/- 0.01 rad/d, with a photospheric shear $\\delta\\Omega$ of $0.21_{-0.03}^{+0.02}$ rad/d. This equates to an equatorial rotation period of ~...

  14. On the origin of the correlations between the accretion luminosity and emission line luminosities in pre-main-sequence stars

    Science.gov (United States)

    Mendigutía, I.; Oudmaijer, R. D.; Rigliaco, E.; Fairlamb, J. R.; Calvet, N.; Muzerolle, J.; Cunningham, N.; Lumsden, S. L.

    2015-09-01

    Correlations between the accretion luminosity and emission line luminosities (Lacc and Lline) of pre-main-sequence (PMS) stars have been published for many different spectral lines, which are used to estimate accretion rates. Despite the origin of those correlations is unknown, this could be attributed to direct or indirect physical relations between the emission line formation and the accretion mechanism. This work shows that all (near-UV/optical/near-IR) Lacc-Lline correlations are the result of the fact that the accretion luminosity and the stellar luminosity (L*) are correlated, and are not necessarily related with the physical origin of the line. Synthetic and observational data are used to illustrate how the Lacc-Lline correlations depend on the Lacc-L* relationship. We conclude that because PMS stars show the Lacc-L* correlation immediately implies that Lacc also correlates with the luminosity of all emission lines, for which the Lacc-Lline correlations alone do not prove any physical connection with accretion but can only be used with practical purposes to roughly estimate accretion rates. When looking for correlations with possible physical meaning, we suggest that Lacc/L* and Lline/L* should be used instead of Lacc and Lline. Finally, the finding that Lacc has a steeper dependence on L* for T Tauri stars than for intermediate-mass Herbig Ae/Be stars is also discussed. That is explained from the magnetospheric accretion scenario and the different photospheric properties in the near-UV.

  15. On the origin of the correlations between the accretion luminosity and emission line luminosities in pre-main sequence stars

    CERN Document Server

    Mendigutía, I; Rigliaco, E; Fairlamb, J R; Calvet, N; Muzerolle, J; Cunningham, N; Lumsden, S L

    2015-01-01

    Correlations between the accretion luminosity and emission line luminosities (L_acc and L_line) of pre-main sequence (PMS) stars have been published for many different spectral lines, which are used to estimate accretion rates. Despite the origin of those correlations is unknown, this could be attributed to direct or indirect physical relations between the emission line formation and the accretion mechanism. This work shows that all (near-UV/optical/near-IR) L_acc-L_line correlations are the result of the fact that the accretion luminosity and the stellar luminosity (L_star) are correlated, and are not necessarily related with the physical origin of the line. Synthetic and observational data are used to illustrate how the L_acc-L_line correlations depend on the L_acc-L_star relationship. We conclude that because PMS stars show the L_acc-L_star correlation immediately implies that L_acc also correlates with the luminosity of all emission lines, for which the L_acc-L_line correlations alone do not prove any phy...

  16. Photometric determination of the mass accretion rate of pre-main sequence stars. IV. Recent star formation in NGC 602

    CERN Document Server

    De Marchi, Guido; Panagia, Nino

    2013-01-01

    We have studied the young stellar populations in NGC 602, in the Small Magellanic Cloud, using a novel method that we have developed to combine Hubble Space Telescope photometry in the V, I, and Halpha bands. We have identified about 300 pre-main sequence (PMS) stars, all of which are still undergoing active mass accretion, and have determined their physical parameters (effective temperature, luminosity, age, mass and mass accretion rate). Our analysis shows that star formation has been present in this field over the last 60 Myr. In addition, we can recognise at least two clear, distinct, and prominent episodes in the recent past: one about 2 Myr ago, but still ongoing in regions of higher nebulosity, and one (or more) older than 30 Myr, encompassing both stars dispersed in the field and two smaller clusters located about 100 arcsec north of the centre of NGC 602. The relative locations of younger and older PMS stars do not imply a causal effect or triggering of one generation on the other. The strength of th...

  17. The influence of radiative core growth on coronal X-ray emission from pre-main sequence stars

    CERN Document Server

    Gregory, Scott G; Davies, Claire L

    2016-01-01

    Pre-main sequence (PMS) stars of mass $\\gtrsim0.35\\,{\\rm M}_\\odot$ transition from hosting fully convective interiors to configurations with a radiative core and outer convective envelope during their gravitational contraction. This stellar structure change influences the external magnetic field topology and, as we demonstrate herein, affects the coronal X-ray emission as a stellar analog of the solar tachocline develops. We have combined archival X-ray, spectroscopic, and photometric data for $\\sim$1000 PMS stars from five of the best studied star forming regions; the ONC, NGC 2264, IC 348, NGC 2362, and NGC 6530. Using a modern, PMS calibrated, spectral type-to-effective temperature and intrinsic colour scale, we deredden the photometry using colours appropriate for each spectral type, and determine the stellar mass, age, and internal structure consistently for the entire sample. We find that PMS stars on Henyey tracks have, on average, lower fractional X-ray luminosities ($L_{\\rm X}/L_\\ast$) than those on ...

  18. The Solar Neighborhood. XXVI. AP Col: The Closest (8.4 pc) Pre-Main-Sequence Star

    CERN Document Server

    Riedel, Adric R; Henry, Todd J; Melis, Carl; Jao, Wei-Chun; Subasavage, John P; 10.1088/0004-6256/142/4/104

    2011-01-01

    We present the results of a multi-technique investigation of the M4.5Ve flare star AP Col, which we discover to be the nearest pre-main-sequence star. These include astrometric data from the CTIO 0.9m, from which we derive a proper motion of 342.0+/-0.5 mas yr^-1, a trigonometric parallax of 119.21+/-0.98 mas (8.39+/-0.07 pc), and photometry and photometric variability at optical wavelengths. We also provide spectroscopic data, including radial velocity (22.4+/-0.3 km s^-1), lithium Equivalent Width (EW) (0.28+/-0.02 A), H-alpha EW (-6.0 to -35 A), {\\it vsini} (11+/-1 km s^-1), and gravity indicators from the Siding Spring 2.3-m WiFeS, Lick 3-m Hamilton echelle, and Keck-I HIRES echelle spectrographs. The combined observations demonstrate that AP Col is the closer of only two known systems within 10 pc of the Sun younger than 100 Myr. Given its space motion and apparent age of 12-50 Myr, AP Col is likely a member of the recently proposed ~40 Myr old Argus/IC 2391 association.

  19. Analysis of flares in the chromosphere and corona of main- and pre-main-sequence M-type stars

    Science.gov (United States)

    Crespo-Chacón, I.

    2015-11-01

    This Ph.D. Thesis revolves around flares on main- and pre-main-sequence M-type stars. We use observations in different wavelength ranges with the aim of analysing the effects of flares at different layers of stellar atmospheres. In particular, optical and X-ray observations are used so that we can study how flares affect, respectively, the chromosphere and the corona of stars. In the optical range we carry out a high temporal resolution spectroscopic monitoring of UV Ceti-type stars aimed at detecting non-white-light flares (the most typical kind of solar flares) in stars other than the Sun. With these data we confirm that non-white-light flares are a frequent phenomenon in UV Ceti-type stars, as observed in the Sun. We study and interpret the behaviour of different chromospheric lines during the flares detected on AD Leo. By using a simplified slab model of flares (Jevremović et al. 1998), we are able to determine the physical parameters of the chromospheric flaring plasma (electron density and electron temperature), the temperature of the underlying source, and the surface area covered by the flaring plasma. We also search for possible relationships between the physical parameters of the flaring plasma and other properties such as the flare duration, area, maximum flux and released energy. This work considerably extends the existing sample of stellar flares analysed with good quality spectroscopy in the optical range. In X-rays we take advantage of the great sensitivity, wide energy range, high energy resolution, and continuous time coverage of the EPIC detectors - on-board the XMMNewton satellite - in order to perform time-resolved spectral analysis of coronal flares. In particular, in the UV Ceti-type star CC Eri we study two flares that are weaker than those typically reported in the literature (allowing us to speculate about the role of flares as heating agents of stellar atmospheres); while in the pre-main-sequence M-type star TWA 11B (with no signatures of

  20. The pre-main-sequence star V1184 Tauri (CB 34V) at the end of prolonged eclipse

    Science.gov (United States)

    Semkov, E. H.; Peneva, S. P.; Ibryamov, S. I.

    2015-10-01

    Aims: V1184 Tau (CB 34V) lies in the field of the Bok globule CB 34 and was discovered as a large amplitude variable in 1993. According to the first hypothesis of the variability of the star, it is a FU Orionis candidate erupted between 1951 and 1993. During subsequent observations, the star manifests large amplitude variability interpreted as obscuration from circumstellar clouds of dust. We included V1184 Tau (CB 34V) in our target list of highly variable pre-main-sequence stars to determine the reasons for the variations in the brightness of this object. Methods: Data from BVRI photometric observations of the young stellar object V1184 Tau, obtained in the period 2008-2015, are presented in the paper. These data are a continuation of our optical photometric monitoring of the star began in 2000 and continuing to date. The photometric observations of V1184 Tau were performed in two observatories with two medium-sized and two small telescopes. Results: Our results indicate that during periods of maximum light the star shows characteristics typical of T Tauri stars. During the observed deep minimum in brightness, however, V1184 Tau is rather similar to UX Orionis objects. The deep drop in brightness began in 2003 ended in 2015 as the star has returned to maximum light. The light curve during the drop is obviously asymmetric as the decrease in brightness lasts two times longer than the rise. The observed colour reverse on the colour-magnitude diagrams is also confirmation of obscuration from circumstellar clouds of dust as a reason for the large amplitude variability in the brightness. Appendix A is available in electronic form at http://www.aanda.org

  1. An IUE Atlas of Pre-Main-Sequence Stars. II. Far-Ultraviolet Accretion Diagnostics in T Tauri Stars

    Science.gov (United States)

    Johns-Krull, Christopher M.; Valenti, Jeff A.; Linsky, Jeffrey L.

    2000-08-01

    We use our ultraviolet (UV) atlas of pre-main-sequence stars constructed from all useful, short-wavelength, low-resolution spectra in the International Ultraviolet Explorer (IUE) satellite Final Archive to analyze the short-wavelength UV properties of 49 T Tauri stars (TTSs). We compare the line and continuum fluxes in these TTSs with each other and with previously published parameters of these systems, including rotation rate, infrared excess, and mass accretion rate. The short-wavelength continuum in the classical TTSs (CTTSs) appears to originate in a ~10,000 K optically thick plasma, while in the naked TTSs (NTTSs-stars without dusty disks) the continuum appears to originate in the stellar atmosphere. We show that all of the TTSs in our sample lie in the regime of ``saturated'' magnetic activity due to their small Rossby numbers. However, while some of the TTSs show emission line surface fluxes consistent with this saturation level, many CTTSs show significantly stronger emission than predicted by saturation. In these stars, the emission line luminosity in the high ionization lines present in the spectrum between 1200 and 2000 Å correlates well with the mass accretion rate. Therefore, we conclude that the bulk of the short-wavelength emission seen in CTTSs results from accretion related processes and not from dynamo-driven magnetic activity. Using CTTSs with known mass accretion rates, we calibrate the relationship between M and LC IV to derive the mass accretion rate for some CTTSs which for various reasons have never had their mass accretion rates measured. Finally, several of the CTTSs show strong emission from molecular hydrogen. While emission from H2 cannot form in gas at a temperature of ~105 K, the strength of the molecular hydrogen emission is nevertheless well correlated with all the other emissions displayed in the IUE short-wavelength bandpass. This suggests that the H2 emission is in fact fluorescent emission pumped by the emission (likely Ly

  2. Effect of accretion on the pre-main-sequence evolution of low-mass stars and brown dwarfs

    Science.gov (United States)

    Vorobyov, Eduard I.; Elbakyan, Vardan; Hosokawa, Takashi; Sakurai, Yuya; Guedel, Manuel; Yorke, Harold

    2017-09-01

    Aims: The pre-main-sequence evolution of low-mass stars and brown dwarfs is studied numerically starting from the formation of a protostellar or proto-brown dwarf seed and taking into account the mass accretion onto the central object during the initial several Myr of evolution. Methods: The stellar evolution was computed using the STELLAR evolution code with recent modifications. The mass accretion rates were taken from numerical hydrodynamics models by computing the circumstellar disk evolution starting from the gravitational collapse of prestellar cloud cores of various mass and angular momentum. The resulting stellar evolution tracks were compared with the isochrones and isomasses calculated using non-accreting models. Results: We find that mass accretion in the initial several Myr of protostellar evolution can have a strong effect on the subsequent evolution of young stars and brown dwarfs. The disagreement between accreting and non-accreting models in terms of the total stellar luminosity L∗, stellar radius R∗, and effective temperature Teff depends on the thermal efficiency of accretion, that is, on the fraction of accretion energy that is absorbed by the central object. The largest mismatch is found for the cold accretion case, in which essentially all accretion energy is radiated away. The relative deviations in L∗ and R∗ in this case can reach 50% for objects 1.0 Myr old, and they remain notable even for objects 10 Myr old. In the hot and hybrid accretion cases, in which a constant fraction of accretion energy is absorbed, the disagreement between accreting and non-accreting models becomes less pronounced, but still remains notable for objects 1.0 Myr old. These disagreements may lead to an incorrect age estimate for objects of (sub-)solar mass when using the isochrones that are based on non-accreting models, as has also been noted previously. We find that objects with strong luminosity bursts exhibit notable excursions in the L∗-Teff diagram

  3. A constraint on the formation timescale of the young open cluster NGC 2264: Lithium abundance of pre-main sequence stars

    CERN Document Server

    Lim, Beomdu; Kim, Jinyoung S; Bessell, Michael S; Hwang, Narae; Park, Byeong-Gon

    2016-01-01

    The timescale of cluster formation is an essential parameter in order to understand the formation process of star clusters. Pre-main sequence (PMS) stars in nearby young open clusters reveal a large spread in brightness. If the spread were considered as a result of a real spread in age, the corresponding cluster formation timescale would be about 5 -- 20 Myr. Hence it could be interpreted that star formation in an open cluster is prolonged for up to a few tens of Myr. However, difficulties in reddening correction, observational errors, and systematic uncertainties introduced by imperfect evolutionary models for PMS stars, can result in an artificial age spread. Alternatively, we can utilize Li abundance as a relative age indicator of PMS star to determine the cluster formation timescale. The optical spectra of 134 PMS stars in NGC 2264 have been obtained with MMT/Hectochelle. The equivalent widths have been measured for 86 PMS stars with a detectable Li line (3500 < T_eff [K] <= 6500). Li abundance unde...

  4. CoRoT 223992193: A new, low-mass, pre-main sequence eclipsing binary with evidence of a circumbinary disk

    CERN Document Server

    Gillen, Edward; McQuillan, Amy; Bouvier, Jerome; Hodgkin, Simon; Alencar, Silvia H P; Terquem, Caroline; Southworth, John; Gibson, Neale P; Cody, Ann Marie; Lendl, Monika; Morales-Calderón, Maria; Favata, Fabio; Stauffer, John; Micela, Giuseppina

    2013-01-01

    We present the discovery of CoRoT 223992193, a double-lined, detached eclipsing binary, comprising two pre-main sequence M dwarfs, discovered by the CoRoT space mission during a 23-day observation of the 3 Myr old NGC 2264 star-forming region. Using multi-epoch optical and near-IR follow-up spectroscopy with FLAMES on the Very Large Telescope and ISIS on the William Herschel Telescope we obtain a full orbital solution and derive the fundamental parameters of both stars by modelling the light curve and radial velocity data. The orbit is circular and has a period of $3.8745745 \\pm 0.0000014$ days. The masses and radii of the two stars are $0.67 \\pm 0.01$ and $0.495 \\pm 0.007$ $M_{\\odot}$ and $1.30 \\pm 0.04$ and $1.11 ~^{+0.04}_{-0.05}$ $R_{\\odot}$, respectively. This system is a useful test of evolutionary models of young low-mass stars, as it lies in a region of parameter space where observational constraints are scarce; comparison with these models indicates an apparent age of $\\sim$3.5-6 Myr. The systemic ve...

  5. Searching for young Jupiter analogs around AP Col: L-band high-contrast imaging of the closest pre-main sequence star

    CERN Document Server

    Quanz, Sascha P; Janson, Markus; Avenhaus, Henning; Meyer, Michael R; Hillenbrand, Lynne A

    2012-01-01

    The nearby M-dwarf AP Col was recently identified by Riedel et al. 2011 as a pre-main sequence star (age 12 - 50 Myr) situated only 8.4 pc from the Sun. The combination of its youth, distance, and intrinsically low luminosity make it an ideal target to search for extrasolar planets using direct imaging. We report deep adaptive optics observations of AP Col taken with VLT/NACO and Keck/NIRC2 in the L-band. Using aggressive speckle suppression and background subtraction techniques, we are able to rule out companions with mass m >= 0.5 - 1M_Jup for projected separations a>4.5 AU, and m >= 2 M_Jup for projected separations as small as 3 AU, assuming an age of 40 Myr using the COND theoretical evolutionary models. Using a different set of models the mass limits increase by a factor of ~2. The observations presented here are the deepest mass-sensitivity limits yet achieved within 20 AU on a star with direct imaging. While Doppler radial velocity surveys have shown that Jovian bodies with close-in orbits are rare ar...

  6. A New Method for the Assessment of Age and Age-Spread of Pre-Main Sequence Stars in Young Stellar Associations of the Magellanic Clouds

    CERN Document Server

    Da Rio, Nicola; Gennaro, Mario

    2010-01-01

    We present a new method for the evaluation of the age and age-spread among pre-main-sequence (PMS) stars in star-forming regions in the Magellanic Clouds, accounting simultaneously for photometric errors, unresolved binarity, differential extinction, stellar variability, accretion and crowding. The application of the method is performed with the statistical construction of synthetic color-magnitude diagrams using PMS evolutionary models. We convert each isochrone into 2D probability distributions of artificial PMS stars in the CMD by applying the aforementioned biases that dislocate these stars from their original CMD positions. A maximum-likelihood technique is then applied to derive the probability for each observed star to have a certain age, as well as the best age for the entire cluster. We apply our method to the photometric catalog of ~2000 PMS stars in the young association LH 95 in the LMC, based on the deepest HST/ACS imaging ever performed toward this galaxy, with a detection limit of V~28, corresp...

  7. Extended Magnetospheres in Pre-main-sequence Evolution: From T Tauri Stars to the Brown Dwarf Limit

    Science.gov (United States)

    Gómez de Castro, Ana I.; Marcos-Arenal, Pablo

    2012-04-01

    Low-mass pre-main-sequence stars, i.e., T Tauri stars (TTSs), strongly radiate at high energies, from X-rays to the ultraviolet (UV). This excess radiation with respect to main-sequence cool stars (MSCSs) is associated with the accretion process, i.e., it is produced in the extended magnetospheres, in the accretion shocks on the stellar surface, and in the outflows. Although evidence of accretion shocks and outflow contribution to the high-energy excess have been recently addressed, there is not an updated revision of the magnetospheric contribution. This article addresses this issue. The UV observations of the TTSs in the well-known Taurus region have been analyzed together with the XMM-Newton observations compiled in the XEST survey. For the first time the high sensitivity of the Hubble Space Telescope UV instrumentation has allowed measurement of the UV line fluxes of TTSs to M8 type. UV- and X-ray-normalized fluxes have been determined to study the extent and properties of the TTS magnetospheres as a class. They have been compared with the atmospheres of the MSCSs. The main results from this analysis are (1) the normalized fluxes of all the tracers are correlated; this correlation is independent of the broad mass range and the hardness of the X-ray radiation field; (2) the TTS correlations are different than the MSCS correlations; (3) there is a very significant excess emission in O I in the TTSs compared with MSCSs that seems to be caused by recombination radiation from the disk atmosphere after photoionization by extreme UV radiation; the Fe II/Mg II recombination continuum has also been detected in several TTSs and most prominently in AA Tau; and (4) the normalized flux of the UV tracers anticorrelates with the strength of the X-ray flux, i.e., the stronger the X-ray surface flux is, the weaker the observed UV flux. This last behavior is counterintuitive within the framework of stellar dynamo theory and suggests that UV emission can be produced in the

  8. Angular momentum transport by internal gravity waves. IV - Wave generation by surface convection zone, from the pre-main sequence to the early-AGB in intermediate mass stars

    CERN Document Server

    Talon, Suzanne

    2008-01-01

    This is the fourth in a series of papers that deal with angular momentum transport by internal gravity waves in stellar interiors. Here, we want to examine the potential role of waves in other evolutionary phases than the main sequence. We study the evolution of a 3Msun Population I model from the pre-main sequence to the early-AGB phase and examine whether waves can lead to angular momentum redistribution and/or element diffusion at the external convection zone boundary. We find that, although waves produced by the surface convection zone can be ignored safely for such a star during the main sequence, it is not the case for later evolutionary stages. In particular, angular momentum transport by internal waves could be quite important at the end of the sub-giant branch and during the early-AGB phase. Wave-induced mixing of chemicals is expected during the early-AGB phase.

  9. MML 53: a new low-mass, pre-main sequence eclipsing binary in the Upper Centarus-Lupus Region discovered by SuperWASP

    CERN Document Server

    Hebb, L; Aigrain, S; Collier-Cameron, A; Hodgkin, S T; Irwin, J M; Maxted, P F L; Pollacco, D; Street, R A; Wilson, D M; Stassun, K G

    2010-01-01

    We announce the discovery of a new low-mass, pre-main sequence eclipsing binary, MML 53. Previous observations of MML 53 found it to be a pre-main sequence spectroscopic multiple associated with the 15-22 Myr Upper Centaurus Lupus cluster. We identify the object as an eclipsing binary for the first time through the analysis of multiple seasons of time series photometry from the SuperWASP transiting planet survey. Re-analysis of a single archive spectrum shows MML 53 to be a spatially unresolved triple system of young stars which all exhibit significant lithium absorption. Two of the components comprise an eclipsing binary with period, P = 2.097891(6) +- 0.000005 and mass ratio, q~0.8. Here, we present the analysis of the discovery data.

  10. THE CLUSTERED NATURE OF STAR FORMATION. PRE-MAIN-SEQUENCE CLUSTERS IN THE STAR-FORMING REGION NGC 602/N90 IN THE SMALL MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Gouliermis, Dimitrios A.; Gennaro, Mario [Max Planck Institute for Astronomy, Koenigstuhl 17, 69117 Heidelberg (Germany); Schmeja, Stefan [Zentrum fuer Astronomie der Universitaet Heidelberg, Institut fuer Theoretische Astrophysik, Albert-Ueberle-Str. 2, 69120 Heidelberg (Germany); Dolphin, Andrew E. [Raytheon Company, P.O. Box 11337, Tucson, AZ 85734 (United States); Tognelli, Emanuele; Prada Moroni, Pier Giorgio [Dipartimento di Fisica ' Enrico Fermi' , Universita di Pisa, largo Pontecorvo 3, Pisa I-56127 (Italy)

    2012-03-20

    Located at the tip of the wing of the Small Magellanic Cloud (SMC), the star-forming region NGC 602/N90 is characterized by the H II nebular ring N90 and the young cluster of pre-main-sequence (PMS) and early-type main-sequence stars NGC 602, located in the central area of the ring. We present a thorough cluster analysis of the stellar sample identified with Hubble Space Telescope/Advanced Camera for Surveys in the region. We show that apart from the central cluster low-mass PMS stars are congregated in 13 additional small, compact sub-clusters at the periphery of NGC 602, identified in terms of their higher stellar density with respect to the average background density derived from star counts. We find that the spatial distribution of the PMS stars is bimodal, with an unusually large fraction ({approx}60%) of the total population being clustered, while the remaining is diffusely distributed in the intercluster area, covering the whole central part of the region. From the corresponding color-magnitude diagrams we disentangle an age difference of {approx}2.5 Myr between NGC 602 and the compact sub-clusters, which appear younger, on the basis of comparison of the brighter PMS stars with evolutionary models, which we accurately calculated for the metal abundance of the SMC. The diffuse PMS population appears to host stars as old as those in NGC 602. Almost all detected PMS sub-clusters appear to be centrally concentrated. When the complete PMS stellar sample, including both clustered and diffused stars, is considered in our cluster analysis, it appears as a single centrally concentrated stellar agglomeration, covering the whole central area of the region. Considering also the hot massive stars of the system, we find evidence that this agglomeration is hierarchically structured. Based on our findings, we propose a scenario according to which the region NGC 602/N90 experiences an active clustered star formation for the last {approx}5 Myr. The central cluster NGC 602 was

  11. Dynamo action and magnetic activity during the pre-main sequence: Influence of rotation and structural changes

    Science.gov (United States)

    Emeriau-Viard, Constance; Brun, Allan Sacha

    2017-10-01

    During the PMS, structure and rotation rate of stars evolve significantly. We wish to assess the consequences of these drastic changes on stellar dynamo, internal magnetic field topology and activity level by mean of HPC simulations with the ASH code. To answer this question, we develop 3D MHD simulations that represent specific stages of stellar evolution along the PMS. We choose five different models characterized by the radius of their radiative zone following an evolutionary track, from 1 Myr to 50 Myr, computed by a 1D stellar evolution code. We introduce a seed magnetic field in the youngest model and then we spread it through all simulations. First of all, we study the consequences that the increase of rotation rate and the change of geometry of the convective zone have on the dynamo field that exists in the convective envelop. The magnetic energy increases, the topology of the magnetic field becomes more complex and the axisymmetric magnetic field becomes less predominant as the star ages. The computation of the fully convective MHD model shows that a strong dynamo develops with a ratio of magnetic to kinetic energy reaching equipartition and even super-equipartition states in the faster rotating cases. Magnetic fields resulting from our MHD simulations possess a mixed poloidal-toroidal topology with no obvious dominant component. We also study the relaxation of the vestige dynamo magnetic field within the radiative core and found that it satisfies stability criteria. Hence it does not experience a global reconfiguration and instead slowly relaxes by retaining its mixed poloidal-toroidal topology.

  12. Investigation of the magnetic field characteristics of Herbig Ae/Be stars: Discovery of the pre-main sequence progenitors of the magnetic Ap/Bp stars

    CERN Document Server

    Wade, G A; Bagnulo, S; Landstreet, J D; Mason, E; Silvester, J; Alecian, E; Böhm, T; Bouret, J C; Catala, C; Donati, J F; Folsom, C; Bale, K

    2006-01-01

    We are investigating the magnetic characteristics of pre-main sequence Herbig Ae/Be stars, with the aim of (1) understanding the origin and evolution of magnetism in intermediate-mass stars, and (2) exploring the influence of magnetic fields on accretion, rotation and mass-loss at the early stages of evolution of A, B and O stars. We have begun by conducting 2 large surveys of Herbig Ae/Be stars, searching for direct evidence of photospheric magnetic fields via the longitudinal Zeeman effect. From observations obtained using FORS1 at the ESO-VLT and ESPaDOnS at the Canada-France-Hawaii Telescope, we report the confirmed detection of magnetic fields in 4 pre-main sequence A- and B-type stars, and the apparent (but as yet unconfirmed) detection of fields in 2 other such stars. We do not confirm the detection of magnetic fields in several stars reported by other authors to be magnetic: HD 139614, HD 144432 or HD 31649. One of the most evolved stars in the detected sample, HD 72106A, shows clear evidence of stron...

  13. Magnetic fields and differential rotation on the pre-main sequence I: The early-G star HD 141943 - brightness and magnetic topologies

    CERN Document Server

    Marsden, S C; Vélez, J C Ramírez; Alecian, E; Brown, C J; Carter, B D; Donati, J F; Dunstone, N; Hart, R; Semel, M; Waite, I A

    2011-01-01

    Spectroscopic and spectropolarimetric observations of the pre-main sequence early-G star HD 141943 were obtained at four observing epochs (in 2006, 2007, 2009 and 2010). The observations were undertaken at the 3.9-m Anglo-Australian Telescope using the UCLES echelle spectrograph and the SEMPOL spectropolarimeter visitor instrument. Brightness and surface magnetic field topologies were reconstructed for the star using the technique of least-squares deconvolution to increase the signal-to-noise of the data. The reconstructed brightness maps show that HD 141943 had a weak polar spot and a significant amount of low latitude features, with little change in the latitude distribution of the spots over the 4 years of observations. The surface magnetic field was reconstructed at three of the epochs from a high order (l <= 30) spherical harmonic expansion of the spectropolarimetric observations. The reconstructed magnetic topologies show that in 2007 and 2010 the surface magnetic field was reasonably balanced betwee...

  14. The clustered nature of star formation. Pre--main-sequence clusters in the star-forming region NGC 602/N90 in the Small Magellanic Cloud

    CERN Document Server

    Gouliermis, Dimitrios A; Dolphin, Andrew E; Gennaro, Mario; Tognelli, Emanuele; Moroni, Pier Giorgio Prada

    2012-01-01

    Located at the tip of the wing of the Small Magellanic Cloud (SMC), the star-forming region NGC602/N90 is characterized by the HII nebular ring N90 and the young cluster of pre--main-sequence (PMS) and early-type main sequence stars NGC602. We present a thorough cluster analysis of the stellar sample identified with HST/ACS camera in the region. We show that apart from the central cluster, low-mass PMS stars are congregated in thirteen additional small compact sub-clusters at the periphery of NGC602. We find that the spatial distribution of the PMS stars is bimodal, with an unusually large fraction (~60%) of the total population being clustered, while the remaining is diffusely distributed in the inter-cluster area. From the corresponding color-magnitude diagrams we disentangle an age-difference of ~2.5Myr between NGC602 and the compact sub-clusters which appear younger. The diffuse PMS population appears to host stars as old as those in NGC602. Almost all detected PMS sub-clusters appear to be centrally conc...

  15. Can we predict the global magnetic topology of a pre-main sequence star from its position in the Hertzsprung-Russell diagram?

    CERN Document Server

    Gregory, S G; Morin, J; Hussain, G A J; Mayne, N J; Hillenbrand, L A; Jardine, M

    2012-01-01

    ZDI studies have shown that the magnetic fields of T Tauri stars can be significantly more complex than a simple dipole and can vary markedly between sources. We collect and summarize the magnetic field topology information obtained to date and present Hertzsprung-Russell (HR) diagrams for the stars in the sample. Intriguingly, the large scale field topology of a given pre-main sequence (PMS) star is strongly dependent upon the stellar internal structure, with the strength of the dipole component of its multipolar magnetic field decaying rapidly with the development of a radiative core. Using the observational data as a basis, we argue that the general characteristics of the global magnetic field of a PMS star can be determined from its position in the HR diagram. Moving from hotter and more luminous to cooler and less luminous stars across the PMS of the HR diagram, we present evidence for four distinct magnetic topology regimes. Stars with large radiative cores, empirically estimated to be those with a core...

  16. Mid-IR spectra of Pre-Main Sequence Herbig stars: an explanation for the non-detections of water lines

    CERN Document Server

    Antonellini, S; Lahuis, F; Woitke, P; Thi, W -F; Meijerink, R; Aresu, G; Spaans, M; Güdel, M; Liebhart, A

    2016-01-01

    The mid-IR detection rate of water lines in disks around Herbig stars disks is about 5\\%, while it is around 50\\% for disks around TTauri stars. The reason for this is still unclear. In this study, we want to find an explanation for the different detection rates between low mass and high mass pre-main-sequence stars (PMSs) in the mid-IR regime. We run disk models with stellar parameters adjusted to spectral types B9 through M2, using the radiation thermo-chemical disk modeling code ProDiMo. We produce convolved spectra at the resolution of Spitzer IRS, JWST MIRI and VLT VISIR spectrographs. We apply random noise derived from typical Spitzer spectra for a direct comparison with observations. The strength of the mid-IR water lines correlates directly with the luminosity of the central star. We explored a small parameter space around a standard disk model, considering dust-to-gas mass ratio, disk gas mass, mixing coefficient for dust settling, flaring index, dust maximum size and size power law distribution inde...

  17. Planetary Construction Zones in Occultation: Eclipses by Circumsecondary and Circumplanetary Disks and a Candidate Eclipse of a Pre-Main Sequence Star in Sco-Cen

    CERN Document Server

    Mamajek, Eric E; Pecaut, Mark; Moolekamp, Fred; Scott, Erin L; Kenworthy, Matthew; Cameron, Andrew Collier; Parley, Neil

    2011-01-01

    The large relative sizes of circumstellar and circumplanetary disks imply that they might be seen in eclipse in stellar light curves. We present photometric and spectroscopic data for a pre-main sequence K5 star (1SWASP J140747.93-394542.6 = ASAS J140748-3945.7), a newly discovered ~0.9 Msun member of the ~16 Myr-old Upper Centaurus-Lupus subgroup of Sco-Cen at a distance of 128+-13 pc. This star exhibited a remarkably long, deep, and complex eclipse event centered on 29 April 2007 (as discovered in SuperWASP photometry, and with portions of the dimming confirmed by ASAS data). At least 5 multi-day dimming events of >0.5 mag are identified, with a >3.3 mag deep eclipse bracketed by two pairs of ~1 mag eclipses symmetrically occurring +-12 days and +-26 days before and after. Hence, significant dimming of the star was taking place on and off over at least a ~54 day period in 2007, and a strong >1 mag dimming event occurring over a ~12 day span. We place a firm lower limit on the period of 850 days (i.e. the o...

  18. XMM-Newton monitoring of the close pre-main-sequence binary AK Sco. Evidence of tide driven filling of the inner gap in the circumbinary disk

    CERN Document Server

    de Castro, Ana I Gomez; Talavera, Antonio; Sytov, A Yu; Bisikalo, D

    2013-01-01

    AK~Sco stands out among pre-main sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit and the strong tides driven by it. AK Sco consists of two F5 type stars that get as close as 11R$_*$ at periastron passage. The presence of a dense ($n_e \\sim 10^{11}$~cm$^{-3}$) extended envelope has been unveiled recently. In this article, we report the results from a XMM-Newton based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of $\\sim 3$ with respect to the apastron values. The X-ray radiation is produced in an optically thin plasma with T$\\sim 6.4\\times 10^{6}$ K and it is found that the N$_H$ column density rises from 0.35$\\times 10^{21}$~cm$^{-2}$ at periastron to 1.11$\\times 10^{21}$~cm$^{-2}$ at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high energy magnetospheric radiation on the circumstellar ...

  19. The multipolar magnetic fields of accreting pre-main-sequence stars: B at the inner disk, B along the accretion flow, and B at the accretion shock

    CERN Document Server

    Gregory, Scott G; Hussain, Gaitee A J

    2016-01-01

    Zeeman-Doppler imaging studies have revealed the complexity of the large-scale magnetic fields of accreting pre-main-sequence stars. All have multipolar magnetic fields with the octupole component being the dominant field mode for many of the stars studied thusfar. Young accreting stars with fully convective interiors often feature simple axisymmetric magnetic fields with dipole components of order a kilo-Gauss (at least those of mass $\\gtrsim0.5\\,{\\rm M}_\\odot$), while those with substantially radiative interiors host more complex non-axisymmetric magnetic fields with dipole components of order a few 0.1 kilo-Gauss. Here, via several simple examples, we demonstrate that i). in most cases, the dipole component alone can be used to estimate the disk truncation radius (but little else); ii) due the presence of higher order magnetic field components, the field strength in the accretion spots is far in excess of that expected if a pure dipole magnetic field is assumed. (Fields of $\\sim$6$\\,{\\rm kG}$ have been mea...

  20. The Multiple Young Stellar Objects of HBC 515: An X-ray and Millimeter-wave Imaging Study in (Pre-main Sequence) Diversity

    CERN Document Server

    Principe, D A; Kastner, J H; Wilner, D; Stelzer, B; Micela, G

    2016-01-01

    We present Chandra X-ray Observatory and Submillimeter Array (SMA) imaging of HBC 515, a system consisting of multiple young stellar objects (YSOs). The five members of HBC 515 represent a remarkably diverse array of YSOs, ranging from the low-mass Class I/II protostar HBC 515B, through Class II and transition disk objects (HBC 515D and C, respectively), to the "diskless", intermediate- mass, pre-main sequence binary HBC 515A. Our Chandra/ACIS imaging establishes that all five components are X-ray sources, with HBC 515A - a subarcsecond-separation binary that is partially resolved by Chandra - being the dominant X-ray source. We detect an X-ray flare associated with HBC 515B. In the SMA imaging, HBC 515B is detected as a strong 1.3 mm continuum emission source; a second, weaker mm continuum source is coincident with the position of the transition disk object HBC 515C. These results strongly support the protostellar nature of HBC 515B, and firmly establish HBC 515A as a member of the rare class of relatively m...

  1. The Gaia-ESO Survey: lithium depletion in the Gamma Velorum cluster and inflated radii in low-mass pre-main-sequence stars

    Science.gov (United States)

    Jeffries, R. D.; Jackson, R. J.; Franciosini, E.; Randich, S.; Barrado, D.; Frasca, A.; Klutsch, A.; Lanzafame, A. C.; Prisinzano, L.; Sacco, G. G.; Gilmore, G.; Vallenari, A.; Alfaro, E. J.; Koposov, S. E.; Pancino, E.; Bayo, A.; Casey, A. R.; Costado, M. T.; Damiani, F.; Hourihane, A.; Lewis, J.; Jofre, P.; Magrini, L.; Monaco, L.; Morbidelli, L.; Worley, C. C.; Zaggia, S.; Zwitter, T.

    2017-01-01

    We show that non-magnetic models for the evolution of pre-main-sequence (PMS) stars cannot simultaneously describe the colour-magnitude diagram (CMD) and the pattern of lithium depletion seen in the cluster of young, low-mass stars surrounding γ2 Velorum. The age of 7.5 ± 1 Myr inferred from the CMD is much younger than that implied by the strong Li depletion seen in the cluster M-dwarfs, and the Li depletion occurs at much redder colours than predicted. The epoch at which a star of a given mass depletes its Li and the surface temperature of that star are both dependent on its radius. We demonstrate that if the low-mass stars have radii ˜10 per cent larger at a given mass and age, then both the CMD and the Li-depletion pattern of the Gamma Velorum cluster are explained at a common age of ≃18-21 Myr. This radius inflation could be produced by some combination of magnetic suppression of convection and extensive cool starspots. Models that incorporate radius inflation suggest that PMS stars, similar to those in the Gamma Velorum cluster, in the range 0.2 30 per cent) than inferred from conventional, non-magnetic models in the Hertzsprung-Russell diagram. Systematic changes of this size may be of great importance in understanding the evolution of young stars, disc lifetimes and the formation of planetary systems.

  2. A High-Resolution Multiband Survey of Westerlund 2 With the Hubble Space Telescope. II. Mass accretion in the Pre-Main Sequence Population

    CERN Document Server

    Zeidler, Peter; Nota, Antonella; Sabbi, Elena; Pasquali, Anna; Tosi, Monica; Bonanos, Alceste Z; Christian, Carol

    2016-01-01

    We present a detailed analysis of the pre-main-sequence (PMS) population of the young star cluster Westerlund~2 (Wd2), the central ionizing cluster of the HII region RCW 49, using data from a high resolution multi-band survey with the Hubble Space Telescope. The data were acquired with the Advanced Camera for Surveys in the F555W, F814W, and F658N filters and with the Wide Field Camera 3 in the F125W, F160W, and F128N filters. We find a mean age of the region of 1.04+-0.72 Myr. The combination of dereddened F555W and F814W photometry in combination with F658N photometry allows us to study and identify stars with H_alpha excess emission. With a careful selection of 240 bona-fide PMS H_alpha excess emitters we were able to determine their H_alpha luminosity, which has a mean value L(H_alpha)=1.67 x 10^{-31} erg s^{-1}. Using the PARSEC 1.2S isochrones to obtain the stellar parameters of the PMS stars we determined a mean mass accretion rate \\dot M_acc=4.43 x 10^{-8} M_sun yr^{-1} per star. A careful analysis of...

  3. CoRoT 223992193: Investigating the variability in a low-mass, pre-main sequence eclipsing binary with evidence of a circumbinary disk

    CERN Document Server

    Gillen, Edward; Terquem, Caroline; Bouvier, Jerome; Alencar, Silvia H P; Gandolfi, Davide; Stauffer, John; Cody, Ann Marie; Venuti, Laura; Almeida, Pedro Viana; Micela, Giuseppina; Favata, Fabio; Deeg, Hans J

    2016-01-01

    CoRoT 223992193 is the only known low-mass, pre-main sequence eclipsing binary that shows evidence of a circumbinary disk. The system displays complex photometric and spectroscopic variability over a range of timescales and wavelengths. Using two optical CoRoT runs, and infrared Spitzer 3.6 and 4.5 $\\mu$m observations (simultaneous with the second CoRoT run), we model the out-of-eclipse light curves. The large scale structure in both CoRoT light curves is consistent with the constructive and destructive interference of starspot signals at two slightly different periods. Using the stellar $v\\sin i$ 's, we infer different rotation periods: the primary is consistent with synchronisation and the secondary is slightly supersynchronous. Comparison of the raw data to the residuals of our spot model in colour-magnitude space indicates additional contributions consistent with variable dust emission and obscuration. We also identify short-duration flux dips preceding secondary eclipse in all three CoRoT and Spitzer ban...

  4. Zodiacal Exoplanets in Time (ZEIT) III: A Neptune-sized planet orbiting a pre-main-sequence star in the Upper Scorpius OB Association

    CERN Document Server

    Mann, Andrew W; Rizzuto, Aaron C; Irwin, Jonathan; Feiden, Gregory A; Gaidos, Eric; Mace, Gregory N; Kraus, Adam L; James, David J; Ansdell, Megan; Charbonneau, David; Covey, Kevin R; Ireland, Michael J; Jaffe, Daniel T; Johnson, Marshall C; Kidder, Benjamin; Vanderburg, Andrew

    2016-01-01

    We confirm and characterize a close-in ($P_\\rm{orb}$ = 5.425 days), super-Neptune sized ($5.04^{+0.34}_{-0.37}$ Earth radii) planet transiting EPIC 205117205 (2MASS J16101473-1919095), a late-type (M3) pre-main sequence ($\\simeq$11 Myr-old) star in the Upper Scorpius subgroup of the Scorpius-Centaurus OB association. The host star has the kinematics of a member of the Upper Scorpius OB association, and its spectrum contains lithium absorption, an unambiguous sign of youth (<20 Myr) in late-type dwarfs. We combine photometry from K2 and the ground-based MEarth project to refine the planet's properties and constrain the average stellar density. We determine EPIC 205117205's bolometric flux and effective temperature from moderate resolution spectra. By utilizing isochrones that include the effects of magnetic fields, we derive a precise (6-7%) radius and mass for the host star, and a stellar age consistent with the established value for Upper Scorpius. Follow-up high-resolution imaging and Doppler spectroscop...

  5. Pre-Main Sequence variables in the VMR-D : identification of T Tauri-like accreting protostars through Spitzer-IRAC variability

    CERN Document Server

    Giannini, T; Elia, D; Strafella, F; De Luca, M; Fazio, G; Marengo, M; Nisini, B; Smith, H A

    2009-01-01

    We present a study of the infrared variability of young stellar objects by means of two Spitzer-IRAC images of the Vela Molecular Cloud D (VMR-D) obtained in observations separated in time by about six months. By using the same space-born IR instrumentation, this study eliminates all the unwanted effects usually unavoidable when comparing catalogs obtained from different instruments. The VMR-D map covers about 1.5 square deg. of a site where star formation is actively ongoing. We are interested in accreting pre-main sequence variables whose luminosity variations are due to intermittent events of disk accretion (i.e. active T Tauri stars and EXor type objects). The variable objects have been selected from a catalog of more than 170,000 sources detected at a S/N ratio > 5. We searched the sample of variables for ones whose photometric properties are close to those of known EXor's. These latter are monitored in a more systematic way than T Tauri stars and the mechanisms that regulate the observed phenomenology a...

  6. The Gaia-ESO Survey: Lithium depletion in the Gamma Velorum cluster and inflated radii in low-mass pre-main-sequence stars

    CERN Document Server

    Jeffries, R D; Franciosini, E; Randich, S; Barrado, D; Frasca, A; Klutsch, A; Lanzafame, A C; Prisinzano, L; Sacco, G G; Gilmore, G; Vallenari, A; Alfaro, E J; Koposov, S E; Pancino, E; Bayo, A; Casey, A R; Costado, M T; Damiani, F; Hourihane, A; Lewis, J; Jofre, P; Magrini, L; Monaco, L; Morbidelli, L; Worley, C C; Zaggia, S; Zwitter, T

    2016-01-01

    We show that non-magnetic models for the evolution of pre-main-sequence (PMS) stars *cannot* simultaneously describe the colour-magnitude diagram (CMD) and the pattern of lithium depletion seen in the cluster of young, low-mass stars surrounding $\\gamma^2$ Velorum. The age of 7.5+/-1 Myr inferred from the CMD is much younger than that implied by the strong Li depletion seen in the cluster M-dwarfs and the Li depletion occurs at much redder colours than predicted. The epoch at which a star of a given mass depletes its Li and the surface temperature of that star are both dependent on its radius. We demonstrate that if the low-mass stars have radii ~10 per cent larger at a given mass and age, then both the CMD and Li depletion pattern of the Gamma Vel cluster are explained at a common age of 18-21 Myr. This radius inflation could be produced by some combination of magnetic suppression of convection and extensive cool starspots. Models that incorporate radius inflation suggest that PMS stars similar to those in t...

  7. High-Precision Radio and Infrared Astrometry of LSPM J1314+1320AB - II: Testing Pre--Main-Sequence Models at the Lithium Depletion Boundary with Dynamical Masses

    CERN Document Server

    Dupuy, Trent J; Rizzuto, Aaron; Mann, Andrew W; Aller, Kimberly; Liu, Michael C; Kraus, Adam L; Berger, Edo

    2016-01-01

    We present novel tests of pre$-$main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of our Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of $0.0885\\pm0.0006$ $M_{\\odot}$ and $0.0875\\pm0.0010$ $M_{\\odot}$ and a parallactic distance of $17.249\\pm0.013$ pc. We also derive component luminosities that are consistent with the system being coeval at an age of $80.8\\pm2.5$ Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first time the theoretical lithium depletion boundary has been tested with ultracool dwarfs of known mass. However, we find that the average evolutionary model-derived effective temperature ($2950\\pm5$ K) is 180 K hotter than we derive from a spectral type$-$$T_{\\rm eff}$ relation based on BT-Settl models ($2770\\pm100$ K). We suggest that the dominant source of this discrepancy is mod...

  8. Zodiacal Exoplanets in Time (ZEIT). III. A Short-period Planet Orbiting a Pre-main-sequence Star in the Upper Scorpius OB Association

    Science.gov (United States)

    Mann, Andrew W.; Newton, Elisabeth R.; Rizzuto, Aaron C.; Irwin, Jonathan; Feiden, Gregory A.; Gaidos, Eric; Mace, Gregory N.; Kraus, Adam L.; James, David J.; Ansdell, Megan; Charbonneau, David; Covey, Kevin R.; Ireland, Michael J.; Jaffe, Daniel T.; Johnson, Marshall C.; Kidder, Benjamin; Vanderburg, Andrew

    2016-09-01

    We confirm and characterize a close-in ({P}{{orb}} = 5.425 days), super-Neptune sized ({5.04}-0.37+0.34 {R}\\oplus ) planet transiting K2-33 (2MASS J16101473-1919095), a late-type (M3) pre-main-sequence (11 Myr old) star in the Upper Scorpius subgroup of the Scorpius-Centaurus OB association. The host star has the kinematics of a member of the Upper Scorpius OB association, and its spectrum contains lithium absorption, an unambiguous sign of youth (\\lt 20 Myr) in late-type dwarfs. We combine photometry from K2 and the ground-based MEarth project to refine the planet’s properties and constrain the host star’s density. We determine K2-33’s bolometric flux and effective temperature from moderate-resolution spectra. By utilizing isochrones that include the effects of magnetic fields, we derive a precise radius (6%-7%) and mass (16%) for the host star, and a stellar age consistent with the established value for Upper Scorpius. Follow-up high-resolution imaging and Doppler spectroscopy confirm that the transiting object is not a stellar companion or a background eclipsing binary blended with the target. The shape of the transit, the constancy of the transit depth and periodicity over 1.5 yr, and the independence with wavelength rule out stellar variability or a dust cloud or debris disk partially occulting the star as the source of the signal; we conclude that it must instead be planetary in origin. The existence of K2-33b suggests that close-in planets can form in situ or migrate within ˜10 Myr, e.g., via interactions with a disk, and that long-timescale dynamical migration such as by Lidov-Kozai or planet-planet scattering is not responsible for all short-period planets.

  9. Photometric Determination of the Mass Accretion Rates of Pre-main-sequence Stars. V. Recent Star Formation in the 30 Dor Nebula

    Science.gov (United States)

    De Marchi, Guido; Panagia, Nino; Beccari, Giacomo

    2017-09-01

    We report on the properties of the low-mass stars that recently formed in the central ∼ 2\\buildrel{ \\prime}\\over{.} 7× 2\\buildrel{ \\prime}\\over{.} 7 of 30 Dor, including the R136 cluster. Using the photometric catalog of De Marchi et al., based on observations with the Hubble Space Telescope, and the most recent extinction law for this field, we identify 1035 bona fide pre-main-sequence (PMS) stars showing {{H}}α excess emission at the 4σ level with an {{H}}α equivalent width of 20 Å or more. We find a wide spread in age spanning the range ∼ 0.1{--}50 {Myr}. We also find that the older PMS objects are placed in front of the R136 cluster and are separated from it by a conspicuous amount of absorbing material, indicating that star formation has proceeded from the periphery into the interior of the region. We derive physical parameters for all PMS stars, including masses m, ages t, and mass accretion rates {\\dot{M}}{acc}. To identify reliable correlations between these parameters, which are intertwined, we use a multivariate linear regression fit of the type {log}{\\dot{M}}{acc}=a× {log}t+b× {log}m+c. The values of a and b for 30 Dor are compatible with those found in NGC 346 and NGC 602. We extend the fit to a uniform sample of 1307 PMS stars with 0.5contract NAS5-26555.

  10. High-precision Radio and Infrared Astrometry of LSPM J1314+1320AB. II. Testing Pre-main-sequence Models at the Lithium Depletion Boundary with Dynamical Masses

    Science.gov (United States)

    Dupuy, Trent J.; Forbrich, Jan; Rizzuto, Aaron; Mann, Andrew W.; Aller, Kimberly; Liu, Michael C.; Kraus, Adam L.; Berger, Edo

    2016-08-01

    We present novel tests of pre-main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of 92.8 ± 0.6 M Jup (0.0885 ± 0.0006 M ⊙) and 91.7 ± 1.0 M Jup (0.0875 ± 0.0010 M ⊙) and a parallactic distance of 17.249 ± 0.013 pc. We find component luminosities consistent with the system being coeval at 80.8 ± 2.5 Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first test of the theoretical lithium depletion boundary using ultracool dwarfs of known mass. However, we find that the evolutionary model-derived average effective temperature (2950 ± 5 K) is 180 K hotter than that given by a spectral type-{T}{eff} relation based on BT-Settl models (2770 ± 100 K). We suggest that the dominant source of this discrepancy is model radii being too small by ≈13%. In a test mimicking the typical application of models by observers, we derive masses on the H-R diagram using luminosity and BT-Settl temperature. The estimated masses are lower by {46}-19+16 % (2.0σ) than we measure dynamically and would imply that this is a system of ≈50 M Jup brown dwarfs, highlighting the large systematic errors possible in H-R diagram properties. This is the first time masses have been measured for ultracool (≥M6) dwarfs displaying spectral signatures of low gravity. Based on features in the infrared, LSPM J1314+1320AB appears to have higher gravity than typical Pleiades and AB Dor members, opposite the expectation given its younger age. The components of LSPM J1314+1320AB are now the nearest, lowest mass pre-main-sequence stars with direct mass measurements. Data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the

  11. XMM-NEWTON MONITORING OF THE CLOSE PRE-MAIN-SEQUENCE BINARY AK SCO. EVIDENCE OF TIDE-DRIVEN FILLING OF THE INNER GAP IN THE CIRCUMBINARY DISK

    Energy Technology Data Exchange (ETDEWEB)

    Gomez de Castro, Ana Ines [S. D. Astronomia y Geodesia and Instituto de Matematica Interdisciplinar, Fac. de CC Matematicas, Universidad Complutense, E-28040 Madrid (Spain); Lopez-Santiago, Javier [Departamento de Astrofisica, Fac de CC Fisicas, Universidad Complutense, E-28040 Madrid (Spain); Talavera, Antonio [European Space Astronomy Center, Villanueva de la Canada, E-28691, Madrid (Spain); Sytov, A. Yu.; Bisikalo, D. [Institute of Astronomy of the Russian Academy of Sciences, Pyatnitskaya St. 48, 109017 Moscow (Russian Federation)

    2013-03-20

    AK Sco stands out among pre-main-sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit, and the strong tides driven by it. AK Sco consists of two F5-type stars that get as close as 11 R{sub *} at periastron passage. The presence of a dense (n{sub e} {approx} 10{sup 11} cm{sup -3}) extended envelope has been unveiled recently. In this article, we report the results from an XMM-Newton-based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of {approx}3 with respect to the apastron values. The X-ray radiation is produced in an optically thin plasma with T {approx} 6.4 Multiplication-Sign 10{sup 6} K and it is found that the N{sub H} column density rises from 0.35 Multiplication-Sign 10{sup 21} cm{sup -2} at periastron to 1.11 Multiplication-Sign 10{sup 21} cm{sup -2} at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high-energy magnetospheric radiation on the circumstellar material. Further evidence of the strong magnetospheric disturbances is provided by the detection of line broadening of 278.7 km s{sup -1} in the N V line with Hubble Space Telescope/Space Telescope Imaging Spectrograph. Numerical simulations of the mass flow from the circumbinary disk to the components have been carried out. They provide a consistent scenario with which to interpret AK Sco observations. We show that the eccentric orbit acts like a gravitational piston. At apastron, matter is dragged efficiently from the inner disk border, filling the inner gap and producing accretion streams that end as ring-like structures around each component of the system. At periastron, the ring-like structures come into contact, leading to angular momentum loss, and thus producing an accretion outburst.

  12. First determination of s-process element abundances in pre-main sequence clusters. Y, Zr, La, and Ce in IC 2391, the Argus association, and IC 2602

    Science.gov (United States)

    D'Orazi, V.; De Silva, G. M.; Melo, C. F. H.

    2017-02-01

    Context. Several high-resolution spectroscopic studies have provided compelling observational evidence that open clusters display a decreasing trend of their barium abundances as a function of the cluster's age. Young clusters (ages ≲ 200 Myr) exhibit significant enhancement in the [Ba/Fe] ratios, at variance with solar-age clusters where the Ba content has been found to be [Ba/Fe] 0 dex. Different viable solutions have been suggested in the literature; nevertheless, a conclusive interpretation of such a peculiar trend has not been found. Interestingly, it is debated whether the other species produced with Ba via s-process reactions follow the same trend with age. Aims: Pre-main sequence clusters (≈10-50 Myr) show the most extreme behaviour in this respect: their [Ba/Fe] ratios can reach 0.65 dex, which is higher than the solar value by a factor of four. Crucially, there are no investigations of the other s-process species for these young stellar populations. In this paper we present the first determination of Y, Zr, La, and Ce in clusters IC 2391, IC 2602, and the Argus association. The main objective of our work is to ascertain whether these elements reveal the same enhancement as Ba. Methods: We have exploited high-resolution, high signal-to-noise spectra in order to derive abundances for Y, Zr, La, and Ce via spectral synthesis calculations. Our sample includes only stars with very similar atmospheric parameters so that internal errors due to star-to-star inhomogeneity are negligible. The chemical analysis was carried out in a strictly differential way, as done in all our previous investigations, to minimise the impact of systematic uncertainties. Results: Our results indicate that, at variance with Ba, all the other s-process species exhibit a solar scaled pattern; these clusters confirm a similar trend discovered in the slightly older local associations (e.g. AB Doradus, Carina-Near), where only Ba exhibit enhanced value with all other s-process species

  13. MEASUREMENT OF SPIN-ORBIT MISALIGNMENT AND NODAL PRECESSION FOR THE PLANET AROUND PRE-MAIN-SEQUENCE STAR PTFO 8-8695 FROM GRAVITY DARKENING

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, Jason W. [Department of Physics, University of Idaho, Moscow, ID 83844-0903 (United States); Van Eyken, Julian C. [Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106-9530 (United States); Jackson, Brian K. [Carnegie Institution of Washington, DTM, 5241 Broad Branch Road, NW Washington, DC 20015-1305 (United States); Ciardi, David R. [NASA Exoplanet Science Institute, Caltech M/S 100-22, Pasadena, CA 91125 (United States); Fortney, Jonathan J., E-mail: jwbarnes@uidaho.edu [Department of Astronomy, University of California Santa Cruz, Santa Cruz, CA 95064 (United States)

    2013-09-01

    PTFO 8-8695b represents the first transiting exoplanet candidate orbiting a pre-main-sequence star (van Eyken et al. 2012, ApJ, 755, 42). We find that the unusual lightcurve shapes of PTFO 8-8695 can be explained by transits of a planet across an oblate, gravity-darkened stellar disk. We develop a theoretical framework for understanding precession of a planetary orbit's ascending node for the case when the stellar rotational angular momentum and the planetary orbital angular momentum are comparable in magnitude. We then implement those ideas to simultaneously and self-consistently fit two separate lightcurves observed in 2009 December and 2010 December. Our two self-consistent fits yield M{sub p} = 3.0 M{sub Jup} and M{sub p} = 3.6 M{sub Jup} for assumed stellar masses of M{sub *} = 0.34 M{sub Sun} and M{sub *} = 0.44 M{sub Sun} respectively. The two fits have precession periods of 293 days and 581 days. These mass determinations (consistent with previous upper limits) along with the strength of the gravity-darkened precessing model together validate PTFO 8-8695b as just the second hot Jupiter known to orbit an M-dwarf. Our fits show a high degree of spin-orbit misalignment in the PTFO 8-8695 system: 69 Degree-Sign {+-} 2 Degree-Sign or 73. Degree-Sign 1 {+-} 0. Degree-Sign 5, in the two cases. The large misalignment is consistent with the hypothesis that planets become hot Jupiters with random orbital plane alignments early in a system's lifetime. We predict that as a result of the highly misaligned, precessing system, the transits should disappear for months at a time over the course of the system's precession period. The precessing, gravity-darkened model also predicts other observable effects: changing orbit inclination that could be detected by radial velocity observations, changing stellar inclination that would manifest as varying vsin i, changing projected spin-orbit alignment that could be seen by the Rossiter-McLaughlin effect, changing

  14. A Tale of Two Anomalies: Depletion, Dispersion, and the Connection between the Stellar Lithium Spread and Inflated Radii on the Pre-main Sequence

    Science.gov (United States)

    Somers, Garrett; Pinsonneault, Marc H.

    2014-07-01

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T eff is nearly universal, and sets in by ~200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

  15. A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

    Energy Technology Data Exchange (ETDEWEB)

    Somers, Garrett; Pinsonneault, Marc H., E-mail: somers@astronomy.ohio-state.edu, E-mail: pinsono@astronomy.ohio-state.edu [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43201 (United States)

    2014-07-20

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T{sub eff} is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

  16. A Tale of Two Anomalies: Depletion, Dispersion, and the Connection Between the Stellar Lithium Spread and Inflated Radii on the Pre-Main Sequence

    CERN Document Server

    Somers, Garrett

    2014-01-01

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed $T_{\\rm eff}$ is nearly universal, and sets in by $\\sim$200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispers...

  17. Impact of initial models and variable accretion rates on the pre-main-sequence evolution of massive and intermediate-mass stars and the early evolution of HII regions

    CERN Document Server

    Haemmerlé, Lionel

    2016-01-01

    Massive star formation requires the accretion of gas at high rate while the star is already bright. Its actual luminosity depends sensitively on the stellar structure. We compute pre-main-sequence tracks for massive and intermediate-mass stars with variable accretion rates and study the evolution of stellar radius, effective temperature and ionizing luminosity, starting at $2\\,M_\\odot$ with convective or radiative structures. The radiative case shows a much stronger swelling of the protostar for high accretion rates than the convective case. For radiative structures, the star is very sensitive to the accretion rate and reacts quickly to accretion bursts, leading to considerable changes in photospheric properties on timescales as short as 100 - 1000 yr. The evolution for convective structures is much less influenced by the instantaneous accretion rate, and produces a monotonically increasing ionizing flux that can be many orders of magnitude smaller than in the radiative case. For massive stars, it results in ...

  18. Impact of initial models and variable accretion rates on the pre-main-sequence evolution of massive and intermediate-mass stars and the early evolution of H II regions

    Science.gov (United States)

    Haemmerlé, Lionel; Peters, Thomas

    2016-05-01

    Massive star formation requires the accretion of gas at high rate while the star is already bright. Its actual luminosity depends sensitively on the stellar structure. We compute pre-main-sequence tracks for massive and intermediate-mass stars with variable accretion rates and study the evolution of stellar radius, effective temperature and ionizing luminosity, starting at 2 M⊙ with convective or radiative structures. The radiative case shows a much stronger swelling of the protostar for high accretion rates than the convective case. For radiative structures, the star is very sensitive to the accretion rate and reacts quickly to accretion bursts, leading to considerable changes in photospheric properties on time-scales as short as 100-1000 yr. The evolution for convective structures is much less influenced by the instantaneous accretion rate, and produces a monotonically increasing ionizing flux that can be many orders of magnitude smaller than in the radiative case. For massive stars, it results in a delay of the H II region expansion by up to 10 000 yr. In the radiative case, the H II region can potentially be engulfed by the star during the swelling, which never happens in the convective case. We conclude that the early stellar structure has a large impact on the radiative feedback during the pre-main-sequence evolution of massive protostars and introduces an important uncertainty that should be taken into account. Because of their lower effective temperatures, our convective models may hint at a solution to an observed discrepancy between the luminosity distribution functions of massive young stellar objects and compact H II regions.

  19. Magnetic fields and differential rotation on the pre-main sequence II: The early-G star HD 141943 - coronal magnetic field, H-alpha emission and differential rotation

    CERN Document Server

    Marsden, S C; Vélez, J C Ramírez; Alecian, E; Brown, C J; Carter, B D; Donati, J F; Dunstone, N; Hart, R; Semel, M; Waite, I A

    2011-01-01

    Spectropolarimetric observations of the pre-main sequence early-G star HD 141943 were obtained at three observing epochs (2007, 2009 and 2010). The observations were obtained using the 3.9-m Anglo-Australian telescope with the UCLES echelle spectrograph and the SEMPOL spectropolarimeter visitor instrument. The brightness and surface magnetic field topologies (given in Paper I) were used to determine the star's surface differential rotation and reconstruct the coronal magnetic field of the star. The coronal magnetic field at the 3 epochs shows on the largest scales that the field structure is dominated by the dipole component with possible evidence for the tilt of the dipole axis shifting between observations. We find very high levels of differential rotation on HD 141943 (~8 times the solar value for the magnetic features and ~5 times solar for the brightness features) similar to that evidenced by another young early-G star, HD 171488. These results indicate that a significant increase in the level of differe...

  20. Estimation of evolutionary distances between nucleotide sequences.

    Science.gov (United States)

    Zharkikh, A

    1994-09-01

    A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process. By using matrix algebra theory, the theoretical foundation of Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984) methods was provided. Extensive computer simulation was used to compare the accuracy and effectiveness of various methods for estimating the evolutionary distance between two nucleotide sequences. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414-422, 1982), and Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) are preferable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutionary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269-285, 1984) method is superior to others.

  1. Thermohaline instability and rotation-induced mixing. III - Grid of stellar models and asymptotic asteroseismic quantities from the pre-main sequence up to the AGB for low- and intermediate-mass stars at various metallicities

    CERN Document Server

    Lagarde, N; Charbonnel, C; Eggenberger, P; Ekström, S; Palacios, A

    2012-01-01

    The availability of asteroseismic constraints for a large sample of stars from the missions CoRoT and Kepler paves the way for various statistical studies of the seismic properties of stellar populations. In this paper, we evaluate the impact of rotation-induced mixing and thermohaline instability on the global asteroseismic parameters at different stages of the stellar evolution from the Zero Age Main Sequence to the Thermally Pulsating Asymptotic Giant Branch to distinguish stellar populations. We present a grid of stellar evolutionary models for four metallicities (Z = 0.0001, 0.002, 0.004, and 0.014) in the mass range between 0.85 to 6.0 Msun. The models are computed either with standard prescriptions or including both thermohaline convection and rotation-induced mixing. For the whole grid we provide the usual stellar parameters (luminosity, effective temperature, lifetimes, ...), together with the global seismic parameters, i.e. the large frequency separation and asymptotic relations, the frequency corre...

  2. Quantitative biostratigraphy and species evolutionary se-quence

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Introduction of species evolutionary sequence into the quantitative biostratigraphy is a significant work, either for studying biologic evolution or for making stratigraphic correlation and reconstructing geologic history. The quantitative biostratigraphy is to determine biostratigraphic event sequences by using probabilistic analysis. The evolutionary sequence systematics can efficiently ascertain species evolutionary sequences. Two methods have been proposed to determine the sequence of species-disappearance events: (1) species extinction events can be closed by last occurrence events using quantitative biostratigraphic analysis; (2) the duration of a species may be approximately replaced by the duration of its parent species. To combine these two methods for determining the sequence of species disappearance is the best way up to now. A consulting standard sequence that consists of the speciation sequence of Permian waagenophylloid corals and the biostratigraphic event sequence of other important fossils in Permian is used as an example. The group spearman rank-correlation test is used to test the consulting standard sequence by comparing four types of calculations and two kinds of sequences and to find abnormal events. Based on the found abnormal events in the test, the consulting standard sequence is revised to deal with different conditions. Sequences of speciation and species-disappearance, and species duration are determined. Application of species evolutionary sequence to quantitative biostratigraphy can largely improve the quality of biostratigraphic event sequence. In stratigraphic correlation, furthermore, event sequences have higher precision than range biozones.

  3. Evolutionary Computation for Realizing Distillation Separation Sequence Optimization Synthesis

    Institute of Scientific and Technical Information of China (English)

    Dong Hongguang; Qin Limin; Wang Kefeng; Yao Pingjing

    2005-01-01

    Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequence, and it is directly applied as the coding method. Genetic operators, which ensure to prohibit illegal filial generations completely, are designed by using the method of graph theory. The crossover operator based on a single parent or two parents is designed successfully. The example shows that the average ratio of search space from evolutionary algorithm with two-parent genetic operation is lower, whereas the rate of successful minimizations from evolutionary algorithm with single parent genetic operation is higher.

  4. Orbital Parameters for a Pre-Main Sequence Binary System

    Science.gov (United States)

    Karnath, Nicole; Prato, L.; Wasserman, L.

    2011-01-01

    The young system VSB 111 was originally classified as a single-lined spectroscopic binary in the star forming region of NGC 2264. Using the Keck II telescope we measured radial velocities for both the primary and secondary components in the infrared. By combining these data with previous visible light observations of the primary star, we derived the period, eccentricity, and other orbital parameters, as well as the mass ratio of the system. With additional information gained from further observations, for example the inclination derived from the angularly resolved orbit, we will eventually obtain the individual stellar masses, necessary to help to calibrate models of young star evolution. Furthermore, by compiling dozens or even hundreds of mass ratios for young binaries we can use mass ratio distributions to improve our understanding of binary star formation. No infrared excess or any other indication of a circumstellar disk is in evidence for VSB 111, indicating that either the accretion rate has dropped to an undetectable value or that this system has aged enough that its disk has dissipated, if originally present. Given the approximately 900 day period of this system, and its relatively high eccentricity, 0.8, the action of the companion could have been responsible for early dissipation of any disk material.

  5. Chemical analysis of 24 dusty (pre-)main-sequence stars

    CERN Document Server

    Acke, B; Acke, Bram; Waelkens, Christoffel

    2004-01-01

    We have analysed the chemical photospheric composition of 24 Herbig Ae/Be and Vega-type stars in search for the lambda Bootis phenomenon. We present the results of the elemental abundances of the sample stars. Some of the stars were never before studied spectroscopically at optical wavelengths. We have determined the projected rotational velocities of our sample stars. Furthermore, we discuss stars that depict a (selective) depletion pattern in detail. HD 4881 and HD 139614 seem to display an overall deficiency. AB Aur and possibly HD 126367 have subsolar values for the iron abundance, but are almost solar in silicon. HD 100546 is the only clear lambda Bootis star in our sample.

  6. Multiple sequence alignment accuracy and evolutionary distance estimation.

    Science.gov (United States)

    Rosenberg, Michael S

    2005-11-23

    Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic position of the additional sequence relative to the first pair changes the accuracy of the initial pair's alignment as well as their estimated evolutionary distance. The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other). Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences. The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.

  7. Universal power law behaviors in genomic sequences and evolutionary models

    CERN Document Server

    Martignetti, L

    2007-01-01

    We study the length distribution of a particular class of DNA sequences known as 5'UTR exons. These exons belong to the messanger RNA of protein coding genes, but they are not coding (they are located upstream of the coding portion of the mRNA) and are thus less constrained from an evolutionary point of view. We show that both in mouse and in human these exons show a very clean power law decay in their length distribution and suggest a simple evolutionary model which may explain this finding. We conjecture that this power law behaviour could indeed be a general feature of higher eukaryotes.

  8. Sequence alignments and pair hidden Markov models using evolutionary history.

    Science.gov (United States)

    Knudsen, Bjarne; Miyamoto, Michael M

    2003-10-17

    This work presents a novel pairwise statistical alignment method based on an explicit evolutionary model of insertions and deletions (indels). Indel events of any length are possible according to a geometric distribution. The geometric distribution parameter, the indel rate, and the evolutionary time are all maximum likelihood estimated from the sequences being aligned. Probability calculations are done using a pair hidden Markov model (HMM) with transition probabilities calculated from the indel parameters. Equations for the transition probabilities make the pair HMM closely approximate the specified indel model. The method provides an optimal alignment, its likelihood, the likelihood of all possible alignments, and the reliability of individual alignment regions. Human alpha and beta-hemoglobin sequences are aligned, as an illustration of the potential utility of this pair HMM approach.

  9. Protein 3D structure computed from evolutionary sequence variation.

    Directory of Open Access Journals (Sweden)

    Debora S Marks

    Full Text Available The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org. This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of

  10. Protein 3D structure computed from evolutionary sequence variation.

    Science.gov (United States)

    Marks, Debora S; Colwell, Lucy J; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures

  11. Evolutionary growth process of highly conserved sequences in vertebrate genomes.

    Science.gov (United States)

    Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

    2012-08-01

    Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Evolutionary relationships of completely sequenced Clostridia species and close relatives.

    Science.gov (United States)

    Kunisawa, Takashi

    2015-11-01

    The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.

  13. Evolutionary insights from suffix array-based genome sequence analysis

    Indian Academy of Sciences (India)

    Anindya Poddar; Nagasuma Chandra; Madhavi Ganapathiraju; K Sekar; Judith Klein-Seetharaman; Raj Reddy; N Balakrishnan

    2007-08-01

    Gene and protein sequence analyses, central components of studies in modern biology are easily amenable to string matching and pattern recognition algorithms. The growing need of analysing whole genome sequences more efficiently and thoroughly, has led to the emergence of new computational methods. Suffix trees and suffix arrays are data structures, well known in many other areas and are highly suited for sequence analysis too. Here we report an improvement to the design of construction of suffix arrays. Enhancement in versatility and scalability, enabled by this approach, is demonstrated through the use of real-life examples. The scalability of the algorithm to whole genomes renders it suitable to address many biologically interesting problems. One example is the evolutionary insight gained by analysing unigrams, bi-grams and higher n-grams, indicating that the genetic code has a direct influence on the overall composition of the genome. Further, different proteomes have been analysed for the coverage of the possible peptide space, which indicate that as much as a quarter of the total space at the tetra-peptide level is left un-sampled in prokaryotic organisms, although almost all tri-peptides can be seen in one protein or another in a proteome. Besides, distinct patterns begin to emerge for the counts of particular tetra and higher peptides, indicative of a ‘meaning’ for tetra and higher n-grams. The toolkit has also been used to demonstrate the usefulness of identifying repeats in whole proteomes efficiently. As an example, 16 members of one COG, coded by the genome of Mycobacterium tuberculosis H37Rv have been found to contain a repeating sequence of 300 amino acids.

  14. Science channel: addressing evolutionary questions using whole genome sequencing

    OpenAIRE

    Kentaro K. Shimizu; Akiyama, Reiko; Hatakeyama, Masaomi

    2015-01-01

    Recently, technical advance in gene analysis opened a new perspective in research on evolution. At the University of Zurich in Switzerland, we visited the Evolutionary Ecological Genomics group and Functional Genomics Center Zurich addressing evolutionary questions using latest technologies.

  15. The sequence, structure and evolutionary features of HOTAIR in mammals

    Science.gov (United States)

    2011-01-01

    Background An increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals

  16. Evolutionary dynamics of insertion sequences in Helicobacter pylori.

    Science.gov (United States)

    Kalia, Awdhesh; Mukhopadhyay, Asish K; Dailide, Giedrius; Ito, Yoshiyki; Azuma, Takeshi; Wong, Benjamin C Y; Berg, Douglas E

    2004-11-01

    Prokaryotic insertion sequence (IS) elements behave like parasites in terms of their ability to invade and proliferate in microbial gene pools and like symbionts when they coevolve with their bacterial hosts. Here we investigated the evolutionary history of IS605 and IS607 of Helicobacter pylori, a genetically diverse gastric pathogen. These elements contain unrelated transposase genes (orfA) and also a homolog of the Salmonella virulence gene gipA (orfB). A total of 488 East Asian, Indian, Peruvian, and Spanish isolates were screened, and 18 and 14% of them harbored IS605 and IS607, respectively. IS605 nucleotide sequence analysis (n = 42) revealed geographic subdivisions similar to those of H. pylori; the geographic subdivision was blurred, however, due in part to homologous recombination, as indicated by split decomposition and homoplasy tests (homoplasy ratio, 0.56). In contrast, the IS607 populations (n = 44) showed strong geographic subdivisions with less homologous recombination (homoplasy ratio, 0.2). Diversifying selection (ratio of nonsynonymous change to synonymous change, >1) was evident in approximately 15% of the IS605 orfA codons analyzed but not in the IS607 orfA codons. Diversifying selection was also evident in approximately 2% of the IS605 orfB and approximately 10% of the IS607 orfB codons analyzed. We suggest that the evolution of these elements reflects selection for optimal transposition activity in the case of IS605 orfA and for interactions between the OrfB proteins and other cellular constituents that potentially contribute to bacterial fitness. Taken together, similarities in IS elements and H. pylori population genetic structures and evidence of adaptive evolution in IS elements suggest that there is coevolution between these elements and their bacterial hosts.

  17. An Evolutionary Machine Learning Framework for Big Data Sequence Mining

    Science.gov (United States)

    Kamath, Uday Krishna

    2014-01-01

    Sequence classification is an important problem in many real-world applications. Unlike other machine learning data, there are no "explicit" features or signals in sequence data that can help traditional machine learning algorithms learn and predict from the data. Sequence data exhibits inter-relationships in the elements that are…

  18. An Evolutionary Machine Learning Framework for Big Data Sequence Mining

    Science.gov (United States)

    Kamath, Uday Krishna

    2014-01-01

    Sequence classification is an important problem in many real-world applications. Unlike other machine learning data, there are no "explicit" features or signals in sequence data that can help traditional machine learning algorithms learn and predict from the data. Sequence data exhibits inter-relationships in the elements that are…

  19. Evolutionary optimization of biopolymers and sequence structure maps

    Energy Technology Data Exchange (ETDEWEB)

    Reidys, C.M.; Kopp, S.; Schuster, P. [Institut fuer Molekulare Biotechnologie, Jena (Germany)

    1996-06-01

    Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is dense and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.

  20. Coelacanth genome sequence reveals the evolutionary history of vertebrate genes.

    Science.gov (United States)

    Noonan, James P; Grimwood, Jane; Danke, Joshua; Schmutz, Jeremy; Dickson, Mark; Amemiya, Chris T; Myers, Richard M

    2004-12-01

    The coelacanth is one of the nearest living relatives of tetrapods. However, a teleost species such as zebrafish or Fugu is typically used as the outgroup in current tetrapod comparative sequence analyses. Such studies are complicated by the fact that teleost genomes have undergone a whole-genome duplication event, as well as individual gene-duplication events. Here, we demonstrate the value of coelacanth genome sequence by complete sequencing and analysis of the protocadherin gene cluster of the Indonesian coelacanth, Latimeria menadoensis. We found that coelacanth has 49 protocadherin cluster genes organized in the same three ordered subclusters, alpha, beta, and gamma, as the 54 protocadherin cluster genes in human. In contrast, whole-genome and tandem duplications have generated two zebrafish protocadherin clusters comprised of at least 97 genes. Additionally, zebrafish protocadherins are far more prone to homogenizing gene conversion events than coelacanth protocadherins, suggesting that recombination- and duplication-driven plasticity may be a feature of teleost genomes. Our results indicate that coelacanth provides the ideal outgroup sequence against which tetrapod genomes can be measured. We therefore present L. menadoensis as a candidate for whole-genome sequencing.

  1. Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise.

    Science.gov (United States)

    Dessimoz, Christophe; Gil, Manuel

    2008-06-23

    The estimation of a distance between two biological sequences is a fundamental process in molecular evolution. It is usually performed by maximum likelihood (ML) on characters aligned either pairwise or jointly in a multiple sequence alignment (MSA). Estimators for the covariance of pairs from an MSA are known, but we are not aware of any solution for cases of pairs aligned independently. In large-scale analyses, it may be too costly to compute MSAs every time distances must be compared, and therefore a covariance estimator for distances estimated from pairs aligned independently is desirable. Knowledge of covariances improves any process that compares or combines distances, such as in generalized least-squares phylogenetic tree building, orthology inference, or lateral gene transfer detection. In this paper, we introduce an estimator for the covariance of distances from sequences aligned pairwise. Its performance is analyzed through extensive Monte Carlo simulations, and compared to the well-known variance estimator of ML distances. Our covariance estimator can be used together with the ML variance estimator to form covariance matrices. The estimator performs similarly to the ML variance estimator. In particular, it shows no sign of bias when sequence divergence is below 150 PAM units (i.e. above ~29% expected sequence identity). Above that distance, the covariances tend to be underestimated, but then ML variances are also underestimated.

  2. Evolutionary conservation of sequence elements controlling cytoplasmic polyadenylylation.

    Science.gov (United States)

    Verrotti, A C; Thompson, S R; Wreden, C; Strickland, S; Wickens, M

    1996-08-20

    Cytoplasmic polyadenylylation is an evolutionarily conserved mechanism involved in the translational activation of a set of maternal messenger RNAs (mRNAs) during early development. In this report, we show by interspecies injections that Xenopus and mouse use the same regulatory sequences to control cytoplasmic poly(A) addition during meiotic maturation. Similarly, Xenopus and Drosophila embryos exploit functionally conserved signals to regulate polyadenylylation during early post-fertilization development. These experiments demonstrate that the sequence elements that govern cytoplasmic polyadenylylation, and hence one form of translational activation, function across species. We infer that the requisite regulatory sequence elements, and likely the trans-acting components with which they interact, have been conserved since the divergence of vertebrates and arthropods.

  3. Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

    Science.gov (United States)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Holden, T.; Lieberman, D.; Cheung, T.

    2013-09-01

    The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary

  4. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

    NARCIS (Netherlands)

    Tyler, B.M.; Tripathy, S.; Zhang, X.; Dehal, P.; Jiang, R.H.Y.; Aerts, A.; Arredondo, F.D.; Baxter, L.; Bensasson, D.; Beynon, J.L.; Chapman, J.; Damasceno, C.M.B.; Dorrance, A.E.; Dou, D.; Dickerman, A.W.; Dubchak, I.L.; Garbelotto, M.; Gijzen, M.; Gordon, S.G.; Govers, F.; Grunwald, N.J.; Huang, W.; Ivors, K.L.; Jones, R.W.; Kamoun, S.; Krampis, K.; Lamour, K.H.; Lee, M.K.; McDonald, W.H.; Medina, M.; Meijer, H.J.G.; Nordberg, E.K.; Maclean, D.J.; Ospina-Giraldo, M.D.; Morris, P.F.; Phuntumart, V.; Putnam, N.H.; Rash, S.; Rose, J.K.C.; Sakihama, Y.; Salamov, A.A.; Savidor, A.; Scheuring, C.F.; Smith, B.M.; Sobral, B.W.S.; Terry, A.; Torto-Alalibo, T.A.; Win, J.; Xu, Z.; Zhang, H.; Grigoriev, I.V.; Rokhsar, D.S.; Boore, J.L.

    2006-01-01

    Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora

  5. πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.

    Science.gov (United States)

    Bielejec, Filip; Lemey, Philippe; Carvalho, Luiz Max; Baele, Guy; Rambaut, Andrew; Suchard, Marc A

    2014-05-07

    Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulation of character evolution along phylogenies. We present a flexible Monte Carlo simulation tool, called πBUSS, that employs the BEAGLE high performance library for phylogenetic computations to rapidly generate large sequence alignments under complex evolutionary models. πBUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. πBUSS may serve as an easy-to-use, standard sequence simulation tool, but the available models and data types are particularly useful to assess the performance of complex BEAST inferences. The connection with BEAST is further strengthened through the use of a common extensible markup language (XML), allowing to specify also more advanced evolutionary models. To support simulation under the latter, as well as to support simulation and analysis in a single run, we also add the πBUSS core simulation routine to the list of BEAST XML parsers. πBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, πBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. Applications are not restricted to the BEAST framework, or even time-measured evolutionary histories, and πBUSS can be connected to various other programs using standard input and output format.

  6. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

    Directory of Open Access Journals (Sweden)

    Grossman Lawrence I

    2007-09-01

    Full Text Available Abstract Background Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence. Results Here we report an online codon-preserved alignment tool (OCPAT that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved. Conclusion The OCPAT program facilitates large-scale evolutionary and

  7. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL; Savidor, Alon [ORNL

    2006-01-01

    Genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, suggest a photosynthetic past and reveal recent massive expansion and diversification of potential pathogenicity gene families. Abstract: Draft genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, have been determined. O mycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms and the presence of many Phytophthora genes of probable phototroph origin support a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors and, in particular, a superfamily of 700 proteins with similarity to known o mycete avirulence genes.

  8. Evolutionary conservation of sequence elements controlling cytoplasmic polyadenylylation.

    OpenAIRE

    1996-01-01

    Cytoplasmic polyadenylylation is an evolutionarily conserved mechanism involved in the translational activation of a set of maternal messenger RNAs (mRNAs) during early development. In this report, we show by interspecies injections that Xenopus and mouse use the same regulatory sequences to control cytoplasmic poly(A) addition during meiotic maturation. Similarly, Xenopus and Drosophila embryos exploit functionally conserved signals to regulate polyadenylylation during early post-fertilizati...

  9. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Tyler, Brett M.; Tripathy, Sucheta; Zhang, Xuemin; Dehal, Paramvir; Jiang, Rays H. Y.; Aerts, Andrea; Arredondo, Felipe D.; Baxter, Laura; Bensasson, Douda; Beynon, JIm L.; Chapman, Jarrod; Damasceno, Cynthia M. B.; Dorrance, Anne E.; Dou, Daolong; Dickerman, Allan W.; Dubchak, Inna L.; Garbelotto, Matteo; Gijzen, Mark; Gordon, Stuart G.; Govers, Francine; Grunwald, NIklaus J.; Huang, Wayne; Ivors, Kelly L.; Jones, Richard W.; Kamoun, Sophien; Krampis, Konstantinos; Lamour, Kurt H.; Lee, Mi-Kyung; McDonald, W. Hayes; Medina, Monica; Meijer, Harold J. G.; Nordberg, Erik K.; Maclean, Donald J.; Ospina-Giraldo, Manuel D.; Morris, Paul F.; Phuntumart, Vipaporn; Putnam, Nicholas J.; Rash, Sam; Rose, Jocelyn K. C.; Sakihama, Yasuko; Salamov, Asaf A.; Savidor, Alon; Scheuring, Chantel F.; Smith, Brian M.; Sobral, Bruno W. S.; Terry, Astrid; Torto-Alalibo, Trudy A.; Win, Joe; Xu, Zhanyou; Zhang, Hongbin; Grigoriev, Igor V.; Rokhsar, Daniel S.; Boore, Jeffrey L.

    2006-04-17

    Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

  10. Evolutionary algorithms for scheduling a flowshop manufacturing cell with sequence dependent family setups

    NARCIS (Netherlands)

    Franca, PM; Gupta, JND; Mendes, AS; Moscato, P; Veltink, KJ

    2005-01-01

    This paper considers the problem of scheduling part families and jobs within each part family in a flowshop manufacturing cell with sequence dependent family setups times where it is desired to minimize the makespan while processing parts (jobs) in each family together. Two evolutionary algorithms-a

  11. Evolutionary algorithms for scheduling a flowshop manufacturing cell with sequence dependent family setups

    NARCIS (Netherlands)

    Franca, PM; Gupta, JND; Mendes, AS; Moscato, P; Veltink, KJ

    This paper considers the problem of scheduling part families and jobs within each part family in a flowshop manufacturing cell with sequence dependent family setups times where it is desired to minimize the makespan while processing parts (jobs) in each family together. Two evolutionary algorithms-a

  12. Quantitative biostratigraphy and species evolutionary se-quence

    Institute of Scientific and Technical Information of China (English)

    XU; Guirong

    2001-01-01

    [1]Liu, T. S., Loess and the Environment, Beijing: China Ocean Press, 1985, 1-251.[2]Chen, L. X., Zhu, Q. G., Luo, H. B. et al., East Asian Monsoon, Beijing: China Meteorology Press, 1991, 28-61.[3]An, Z. S., Liu, T. S., Lu, Y. C. et al., The long-term palaeomonsoon variation recorded by the loess-palaeosol sequence in central China, Quaternary International, 1990, (7/8): 91-95.[4]Guo, Z. T., Liu, T. S., Fedoroff, N. et al., Shift of the monsoon intensity on the Loess Plateau at ca. 0.85 MaBP, Chinese Science Bulletin, 1993, 38(2): 586-591.[5]Chen, J., An, Z. S., Wang, Y. J. et al., Distributions of Rb and Sr in the Luochuan loess-paleosol sequence of China during the last 800 ka: Implications for paleomonsoon variations, Science in China, Ser. D, 1999, 42(3): 225-232.[6]Chen, J., Wang, Y. J., Ji, J. F. et al., Rb/Sr variations and its climatic stratigraphical significance of a loess-paleosol profile from Luochuan, Shaanxi Province, Quaternary Sciences (in Chinese), 1999, 19(4): 350-356.[7]Guo, Z. T.,Liu, T. S., Fedoroff, N. et al., Climate extremes in loess of China coupled with the strength of deep-water for-mation in the North Atlantic, Global and Planetary Change, 1998, 18: 113-128.[8]Guo, Z. T., Liu, T. S., An, Z. S., Paleosols of the last 0.15 Ma in the Weinan loess section and their paleoclimate signifi-cance, Quaternary Sciences (in Chinese), 1994, 14(3): 256-269.[9]Guo, Z, T,, Fedoroff, N., Liu, T. S., Micromorphology of the loess-paleosol sequence of the last 130 ka in China and pa-leoclimatic event, Science in China (in Chinese), Ser. D, 1996, 26(3): 392-398.[10]Guo, Z., Liu, T., Guiot, J., et al., High frequency pulses of East Asian monsoon climate in the last two glaciations: Link with the North Atlantic, Climate Dynamics, 1996, 12: 701-709.[11]Guo, Z. T., Peng, S. Z., Wei, L. Y. et al., Weathering signals of Millennial-Scale oscillations of the East Asian Summer monsoon over the last 220 ka, Chinese Science

  13. Evolutionary evidence for alternative structure in RNA sequence co-variation.

    Directory of Open Access Journals (Sweden)

    Justin Ritz

    Full Text Available Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches, a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. We set out to characterize the evolutionary co-variation supporting alternative conformations in riboswitches to determine the extent to which alternative secondary structures are conserved. We found strong co-variation support for the terminator, P1, and anti-terminator stems in the purine riboswitch by extending alignments to include terminator sequences. When we performed Boltzmann suboptimal sampling on purine riboswitch sequences with terminators we found that these sequences appear to have evolved to favor specific alternative conformations. We extended our analysis of co-variation to classic alignments of group I/II introns, tRNA, and other classes of riboswitches. In a majority of these RNAs, we found evolutionary evidence for alternative conformations that are compatible with the Boltzmann suboptimal ensemble. Our analyses suggest that alternative conformations are selected for and thus likely play functional roles in even the most structured of RNAs.

  14. Accretion in the Rho-Oph pre-main sequence stars

    CERN Document Server

    Natta, A; Testi, L

    2006-01-01

    The aim of this paper is to provide a measurement of the mass accretion rate in a large, complete sample of objects in the core of the star forming region Rho-Oph. The sample includes most of the objects (104 out of 111) with evidence of a circumstellar disk from mid-infrared photometry; it covers a stellar mass range from about 0.03 to 3 Msun and it is complete to a limiting mass of ~0.05 Msun. We used J and K-band spectra to derive the mass accretion rate of each object from the intensity of the hydrogen recombination lines, Pab or Brg. For comparison, we also obtained similar spectra of 35 diskless objects. The results show that emission in these lines is only seen in stars with disks, and can be used as an indicator of accretion. However, the converse does not hold, as about 50% of our disk objects do not have detectable line emission. The measured accretion rates show a strong correlation with the mass of the central object (Macc ~ Mstar^1.8+-0.2) and a large spread, of two orders of magnitude at least, ...

  15. Empirical Tests of Pre-Main-Sequence Stellar Evolution Models with Eclipsing Binaries

    CERN Document Server

    Stassun, Keivan G; Torres, Guillermo

    2014-01-01

    We examine the performance of standard PMS stellar evolution models against the accurately measured properties of a benchmark sample of 26 PMS stars in 13 EB systems. We provide a definitive compilation of all fundamental properties for the EBs. We also provide a definitive compilation of the various PMS model sets. In the H-R diagram, the masses inferred for the individual stars by the models are accurate to better than 10% above 1 Msun, but below 1 Msun they are discrepant by 50-100%. We find evidence that the failure of the models to match the data is linked to the triples in the EB sample; at least half of the EBs possess tertiary companions. Excluding the triples, the models reproduce the stellar masses to better than ~10% in the H-R diagram, down to 0.5 Msun, below which the current sample is fully contaminated by tertiaries. We consider several mechanisms by which a tertiary might cause changes in the EB properties and thus corrupt the agreement with stellar model predictions. We show that the energies...

  16. YSOVAR: Six Pre-main-sequence Eclipsing Binaries in the Orion Nebula Cluster

    Science.gov (United States)

    2012-06-25

    includes background subtraction, cosmic -hit removal, flat-fielding, and wavelength calibration. 23 http://www2.keck.hawaii.edu/inst/nirspec-old/redspec...Inclination and combined radius are highly degenerated; inclination and temperature ratio are less so, but also provide weaker constraints. (A color version of...example, the model isochrones of Siess et al. (2000) predict a radius sum of 11.1–14.5R for ages in the range of 0.3–2 Myr. 5.2. ISOY J0535−0447 ISOY

  17. Active Phenomena in the Pre-main Sequence Star AB AUR

    Science.gov (United States)

    Praderie, F.; Simon, T.; Boesgaard, A. M.; Felenbok, P.; Catala, C.; Czarny, J.; Talavera, A.

    1985-01-01

    The Herbig Ae star AB Aur presents short time scale variability in the Mg II and Ca II resonance lines. A qualitative model of the expanding envelope, involving fast and slow streams in a co-rotating structure, is proposed to explain the Mg II spectral variability.

  18. Old pre-main-sequence Stars: Disc reformation by Bondi-Hoyle accretion

    CERN Document Server

    Scicluna, P; Dale, J E; Testi, L

    2014-01-01

    Young stars show evidence of accretion discs which evolve quickly and disperse with an e-folding time of $\\sim$ 3Myr. This is in striking contrast with recent observations that suggest evidence for numerous $>30$ Myr old stars with an accretion disc in large star-forming complexes. We consider whether these observations of apparently old accretors could be explained by invoking Bondi-Hoyle accretion to rebuild a new disc around these stars during passage through a clumpy molecular cloud. We combine a simple Monte Carlo model to explore the capture of mass by such systems with a viscous evolution model to infer the levels of accretion that would be observed. We find that a significant fraction of stars may capture enough material via the Bondi-Hoyle mechanism to rebuild a disc of mass $\\gtrsim$ 1 minimum-mass solar nebula, and $\\lesssim 10\\%$ accrete at observable levels at any given time. A significant fraction of the observed old accretors may be explained with our proposed mechanism. Such accretion may prov...

  19. Pre-main sequence stars with disks in the Eagle Nebula observed in scattered light

    CERN Document Server

    Guarcello, M G; Micela, G; Peres, G; Prisinzano, L; Sciortino, S

    2010-01-01

    NGC6611 and its parental cloud, the Eagle Nebula (M16), are well-studied star-forming regions, thanks to their large content of both OB stars and stars with disks and the observed ongoing star formation. We identified 834 disk-bearing stars associated with the cloud, after detecting their excesses in NIR bands from J band to 8.0 micron. In this paper, we study in detail the nature of a subsample of disk-bearing stars that show peculiar characteristics. They appear older than the other members in the V vs. V-I diagram, and/or they have one or more IRAC colors at pure photospheric values, despite showing NIR excesses, when optical and infrared colors are compared. We confirm the membership of these stars to M16 by a spectroscopic analysis. The physical properties of these stars with disks are studied by comparing their spectral energy distributions (SEDs) with the SEDs predicted by models of T-Tauri stars with disks and envelopes. We show that the age of these stars estimated from the V vs. V-I diagram is unrel...

  20. An unusual very low-mass high-amplitude pre-main sequence periodic variable

    CERN Document Server

    Rodriguez-Ledesma, Maria V; Ibrahimov, Mansur; Messina, Sergio; Parihar, Padmakar; Hessman, Frederic; de Oliveira, Catarina Alves; Herbst, William

    2012-01-01

    We have investigated the nature of the variability of CHS7797, an unusual periodic variable in the Orion Nebula Cluster. An extensive I-band photometric data set of CHS7797 was compiled between 2004-2010 using various telescopes. Further optical data have been collected in R and z' bands. In addition, simultaneous observations of the ONC region including CHS7797 were performed in the I, J, Ks and IRAC [3.6] and [4.5] bands over a time interval of about 40d. CHS7797 shows an unusual large-amplitude variation of about 1.7 mag in the R, I, and z' bands with a period 17.786. The amplitude of the brightness modulation decreases only slightly at longer wavelengths. The star is faint during 2/3 of the period and the shape of the phased light-curves for seven different observing seasons shows minor changes and small-amplitude variations. Interestingly, there are no significant colour-flux correlations for wavelengths smaller than 2microns, while the object becomes redder when fainter at longer wavelengths. CHS7797 ha...

  1. The pre-main sequence population of NGC 6530 in M8

    Directory of Open Access Journals (Sweden)

    J. I. Arias

    2006-01-01

    Full Text Available Presentamos los resultados de una investigaci on de probables miembros d ebiles del c umulo abierto muy joven NGC 6530 en M8, basados en espectroscop a de resoluci on intermedia obtenida con el telescopio Magallanes I de 6.5 m del Observatorio Las Campanas. El an alisis de los espectros condujo al descubrimiento de 39 nuevas estrellas de pre-secuencia principal en la regi on. De acuerdo a los tipos espectrales, y a la presencia de l neas de emisi on y de l nea de absorci on de litio, identi camos 30 estrellas T-Tauri cl asicas, 7 estrellas T-Tauri d ebiles y dos objetos Herbig Ae/Be. Utilizando magnitudes infrarrojas de 2MASS y de nuestro trabajo previo, y las huellas evolutivas de Palla & Stahler (1999, estimamos las masas y edades de estas estrellas. Encontramos que casi todas las estrellas de nuestra muestra son m as j ovenes que 3 106 a~nos y abarcan un intervalo de masas de entre 0.8 y 2.0 M .

  2. Pre-main-sequence population in NGC 1893 region: X-ray properties

    CERN Document Server

    Pandey, A K; Yadav, Ram Kesh; Richichi, Andrea; Lata, Sneh; Pandey, J C; Ojha, D K; Chen, W P

    2013-01-01

    Continuing the attempt to understand the properties of the stellar content in the young cluster NGC 1893 we have carried out a comprehensive multi-wavelength study of the region. The present study focuses on the X-ray properties of T-Tauri Stars (TTSs) in the NGC 1893 region. We found a correlation between the X-ray luminosity, $L_X$, and the stellar mass (in the range 0.2$-$2.0 \\msun) of TTSs in the NGC 1893 region, similar to those reported in some other young clusters, however the value of the power-law slope obtained in the present study ($\\sim$ 0.9) for NGC 1893 is smaller than those ($\\sim$1.4 - 3.6) reported in the case of TMC, ONC, IC 348 and Chameleon star forming regions. However, the slope in the case of Class III sources (Weak line TTSs) is found to be comparable to that reported in the case of NGC 6611 ($\\sim$ 1.1). It is found that the presence of circumstellar disks has no influence on the X-ray emission. The X-ray luminosity for both CTTSs and WTTSs is found to decrease systematically with age...

  3. The Structure of the Accretion Flow on pre-main-sequence stars

    Science.gov (United States)

    Calvet, Nuria

    1999-07-01

    We propose to test an essential prediction of the magnetospheric accretion model for T Tauri stars. STIS echelle spectra will be used to search for the relatively narrow high-temperature emission lines that must result from the magnetospheric accretion shock, but are not expected in the previous, alternative boundary layer model. By combining the results from high temperature {10^5 K} lines, accessible only with HST, with optical lines and optical-UV continuum emission, we will develop physically self-consistent models of accretion shock structure. The geometrically distribution of the emitting gas as derived from our results will test theories of mass-loading of magnetic field lines at the magnetosphere-disk interface. Analysis of the UV emission lines will also provide improved calibrations between ultraviolet continuum emission and accretion luminosities, and thus improve estimates of mass accretion rates for T Tauri stars.

  4. Extreme value statistics for two-dimensional convective penetration in a pre-main sequence star

    Science.gov (United States)

    Pratt, J.; Baraffe, I.; Goffrey, T.; Constantino, T.; Viallet, M.; Popov, M. V.; Walder, R.; Folini, D.

    2017-08-01

    Context. In the interior of stars, a convectively unstable zone typically borders a zone that is stable to convection. Convective motions can penetrate the boundary between these zones, creating a layer characterized by intermittent convective mixing, and gradual erosion of the density and temperature stratification. Aims: We examine a penetration layer formed between a central radiative zone and a large convection zone in the deep interior of a young low-mass star. Using the Multidimensional Stellar Implicit Code (MUSIC) to simulate two-dimensional compressible stellar convection in a spherical geometry over long times, we produce statistics that characterize the extent and impact of convective penetration in this layer. Methods: We apply extreme value theory to the maximal extent of convective penetration at any time. We compare statistical results from simulations which treat non-local convection, throughout a large portion of the stellar radius, with simulations designed to treat local convection in a small region surrounding the penetration layer. For each of these situations, we compare simulations of different resolution, which have different velocity magnitudes. We also compare statistical results between simulations that radiate energy at a constant rate to those that allow energy to radiate from the stellar surface according to the local surface temperature. Results: Based on the frequency and depth of penetrating convective structures, we observe two distinct layers that form between the convection zone and the stable radiative zone. We show that the probability density function of the maximal depth of convective penetration at any time corresponds closely in space with the radial position where internal waves are excited. We find that the maximal penetration depth can be modeled by a Weibull distribution with a small shape parameter. Using these results, and building on established scalings for diffusion enhanced by large-scale convective motions, we propose a new form for the diffusion coefficient that may be used for one-dimensional stellar evolution calculations in the large Péclet number regime. These results should contribute to the 321D link.

  5. The discovery of a low mass, pre-main-sequence stellar association around $\\gamma$ Velorum

    CERN Document Server

    Pozzo, M; Naylor, T; Totten, E J; Harmer, S; Kenyon, M E

    2000-01-01

    We report the serendipitous discovery of a population of low mass, pre-mainsequence stars (PMS) in the direction of the Wolf-Rayet/O-star binary systemgamma^{2} Vel and the Vela OB2 association. We argue that gamma^{2} Vel and thelow mass stars are truly associated, are approximately coeval and that both areat distances between 360-490 pc, disagreeing at the 2 sigma level with therecent Hipparcos parallax of gamma^{2} Vel, but consistent with older distanceestimates. Our results clearly have implications for the physical parameters ofthe gamma^{2} Vel system, but also offer an exciting opportunity to investigatethe influence of high mass stars on the mass function and circumstellar disclifetimes of their lower mass PMS siblings.

  6. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    Science.gov (United States)

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.

  7. Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.

    Science.gov (United States)

    Marsh, Joseph A; Teichmann, Sarah A

    2014-02-01

    Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely related to local protein flexibility and disorder, large-scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution.

  8. mtDNA sequences suggest a recent evolutionary divergence for Beringian and Northern American populations

    Energy Technology Data Exchange (ETDEWEB)

    Shields, G.F.; Schmiechen, A.M.; Reed, J.K. (Univ. of Alaska, Fairbanks, AK (United States)); Frazier, B.L.; Redd, A.; Ward, R.H. (Univ. of Utah, Salt Lake City, UT (United States)); Voevoda, M.I. (Institute of Internal Medicine, Novosibirsk (Russian Federation))

    1993-09-01

    Conventional descriptions of the pattern and process of human entry into the New World from Asia are incomplete and controversial. In order to gain an evolutionary insight into this process, the authors have sequenced the control region of mtDNA in samples of contemporary tribal populations of eastern Siberia, Alaska, and Greenland and have compared them with those of Amerind speakers of the Pacific Northwest and with those of the Altai of central Siberia. Specifically, they have analyzed sequence diversity in 33 mitochondiral lineages identified in 90 individuals belonging to five Circumpolar populations of Beringia, North America, and Greenland: Chukchi from Siberia, Inupiaq Eskimos and Athapaskans from Alaska, Eskimos from West Greenland, and Haida from Canada. Hereafter, these five populations are referred to as Circumarctic peoples'. These data were then compared with the sequence diversity in 47 mitochondrial lineages identified in a sample of 145 individuals from three Amerind-speaking tribes (Bella Coola, Nuu-Chah-Nulth, and Yakima) of the Pacific Northwest, plus 16 mitrochondrial lineages identified in a sample of 17 Altai from central Siberia. Sequence diversity within and among Circumarctic populations is considerably less than the sequence diversity observed within and among the three Amerind tribes. The similarity of sequences found among the geographically dispersed Circumarctic groups, plus the small values of mean pairwise sequence differences within Circumarctic populations, suggest a recent and rapid evolutionary radiation of these populations. In addition, Circumarctic populations lack the 9-bp deletion which has been used to trace various migrations out of Asia, while populations of southeastern Siberia possess this deletion. On the basis of these observations, while the evolutionary affinities of Native Americans extend west to the Circumarctic populations of eastern Siberia, they do not include the Altai of central Siberia.

  9. Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

    OpenAIRE

    Chan, Y.; Roos, C.; Inoue-Murayama, M.; Inoue, E; Shih, C.; Pei, K.; Vigilant, L.

    2013-01-01

    Background Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. Results To inve...

  10. Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications

    Science.gov (United States)

    Herzog, Michel; Maroteaux, Luc

    1986-01-01

    We present the complete sequence of the nuclear-encoded small-ribosomal-subunit RNA inferred from the cloned gene sequence of the dinoflagellate Prorocentrum micans. The dinoflagellate 17S rRNA sequence of 1798 nucleotides is contained in a family of 200 tandemly repeated genes per haploid genome. A tentative model of the secondary structure of P. micans 17S rRNA is presented. This sequence is compared with the small-ribosomal-subunit rRNA of Xenopus laevis (Animalia), Saccharomyces cerevisiae (Fungi), Zea mays (Planta), Dictyostelium discoideum (Protoctista), and Halobacterium volcanii (Monera). Although the secondary structure of the dinoflagellate 17S rRNA presents most of the eukaryotic characteristics, it contains sufficient archaeobacterial-like structural features to reinforce the view that dinoflagellates branch off very early from the eukaryotic lineage. PMID:16578795

  11. MultiSeq: unifying sequence and structure data for evolutionary analysis

    Directory of Open Access Journals (Sweden)

    Wright Dan

    2006-08-01

    Full Text Available Abstract Background Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. Conclusion MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural

  12. Beyond the Main Sequence: Testing the accuracy of stellar masses predicted by the PARSEC evolutionary tracks

    CERN Document Server

    Ghezzi, Luan

    2015-01-01

    Characterizing the physical properties of exoplanets, and understanding their formation and orbital evolution requires precise and accurate knowledge of the physical properties of their host stars. Accurately measuring stellar mass is particularly important because the masses of host stars likely influence planet occurrence and the architectures of planetary systems observed today. Single main-sequence stars typically have masses estimated from evolutionary tracks, which generally provide accurate results due to their extensive empirical calibration. However, the validity of this method for subgiants and giants has been called into question, with suggestions that the evolutionary models could contain systematic errors that would cause mass estimates of these evolved stars to be overestimated. We investigate these concerns using a sample of 59 benchmark evolved stars with model-independent masses (from binary systems or asteroseismology) obtained from the extant literature. We find very good agreement between ...

  13. Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences.

    Science.gov (United States)

    Nguyen Ba, Alex N; Strome, Bob; Hua, Jun Jie; Desmond, Jonathan; Gagnon-Arsenault, Isabelle; Weiss, Eric L; Landry, Christian R; Moses, Alan M

    2014-12-01

    Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication.

  14. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Directory of Open Access Journals (Sweden)

    John A Capra

    2009-12-01

    Full Text Available Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/.

  15. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Science.gov (United States)

    Capra, John A; Laskowski, Roman A; Thornton, Janet M; Singh, Mona; Funkhouser, Thomas A

    2009-12-01

    Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/).

  16. Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

    Science.gov (United States)

    2013-01-01

    Background Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. Results To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. Conclusions Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera. PMID:23586586

  17. 2-D Radiative Transfer in Protostellar Envelopes: II. An Evolutionary Sequence

    OpenAIRE

    Whitney, Barbara A.; Wood, Kenneth; Bjorkman, J. E.; Cohen, Martin

    2003-01-01

    We present model spectral energy distributions, colors, polarization, and images for an evolutionary sequence of a low-mass protostar from the early collapse stage (Class 0) to the remnant disk stage (Class III). We find a substantial overlap in colors and SEDs between protostars embedded in envelopes (Class 0-I) and T Tauri disks (Class II), especially at mid-IR wavelengths. Edge-on Class I-II sources show double-peaked spectral energy distributions, with a short-wavelength hump due to scatt...

  18. Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison

    Directory of Open Access Journals (Sweden)

    Venclovas Česlovas

    2010-02-01

    Full Text Available Abstract Background Detection of common evolutionary origin (homology is a primary means of inferring protein structure and function. At present, comparison of protein families represented as sequence profiles is arguably the most effective homology detection strategy. However, finding the best way to represent evolutionary information of a protein sequence family in the profile, to compare profiles and to estimate the biological significance of such comparisons, remains an active area of research. Results Here, we present a new homology detection method based on sequence profile-profile comparison. The method has a number of new features including position-dependent gap penalties and a global score system. Position-dependent gap penalties provide a more biologically relevant way to represent and align protein families as sequence profiles. The global score system enables an analytical solution of the statistical parameters needed to estimate the statistical significance of profile-profile similarities. The new method, together with other state-of-the-art profile-based methods (HHsearch, COMPASS and PSI-BLAST, is benchmarked in all-against-all comparison of a challenging set of SCOP domains that share at most 20% sequence identity. For benchmarking, we use a reference ("gold standard" free model-based evaluation framework. Evaluation results show that at the level of protein domains our method compares favorably to all other tested methods. We also provide examples of the new method outperforming structure-based similarity detection and alignment. The implementation of the new method both as a standalone software package and as a web server is available at http://www.ibt.lt/bioinformatics/coma. Conclusion Due to a number of developments, the new profile-profile comparison method shows an improved ability to match distantly related protein domains. Therefore, the method should be useful for annotation and homology modeling of uncharacterized

  19. A new hypothesis of squamate evolutionary relationships from nuclear and mitochondrial DNA sequence data

    Energy Technology Data Exchange (ETDEWEB)

    Townsend, Ted M.; Larson, Allan; Louis, Edward; Macey, J. Robert

    2004-05-19

    Squamate reptiles serve as model systems for evolutionary studies of a variety of morphological and behavioral traits, and phylogeny is crucial to many generalizations derived from such studies. Specifically, the traditional dichotomy between Iguania and Scleroglossa has been correlated with major evolutionary shifts within Squamata. We present a molecular phylogenetic study of squamates using DNA sequence data from the nuclear genes RAG-1 and c-mos and the mitochondrial ND2 region, sampling all major clades and most major subclades. Monophyly of Iguania, Anguimorpha, and almost all currently recognized squamate families is strongly supported. However, monophyly is rejected for Scleroglossa, Varanoidea, and several other higher taxa, and Iguania is highly nested within Squamata. Limblessness evolved independently in snakes, dibamids, and amphisbaenians, suggesting widespread morphological convergence or parallelism in limbless, burrowing forms. Amphisbaenians are the sister group of lacertids, and snakes are grouped with iguanians and anguimorphs. Dibamids diverged early in squamate evolutionary history. Xantusiidae is the sister taxon of Cordylidae. Studies of functional tongue morphology and feeding mode have found significant differences between Scleroglossa and Iguania, and our finding of a nonmonophyletic Scleroglossa and a highly nested Iguania suggest that similar states evolved separately in Sphenodon and Iguania, and that jaw prehension is the ancestral feeding mode in squamates.

  20. Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm

    KAUST Repository

    Wong, Ka Chun

    2011-02-05

    Protein-DNA bindings are essential activities. Understanding them forms the basis for further deciphering of biological and genetic systems. In particular, the protein-DNA bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) play a central role in gene transcription. Comprehensive TF-TFBS binding sequence pairs have been found in a recent study. However, they are in one-to-one mappings which cannot fully reflect the many-to-many mappings within the bindings. An evolutionary algorithm is proposed to learn generalized representations (many-to-many mappings) from the TF-TFBS binding sequence pairs (one-to-one mappings). The generalized pairs are shown to be more meaningful than the original TF-TFBS binding sequence pairs. Some representative examples have been analyzed in this study. In particular, it shows that the TF-TFBS binding sequence pairs are not presumably in one-to-one mappings. They can also exhibit many-to-many mappings. The proposed method can help us extract such many-to-many information from the one-to-one TF-TFBS binding sequence pairs found in the previous study, providing further knowledge in understanding the bindings between TFs and TFBSs. © 2011 Springer-Verlag.

  1. The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

    Science.gov (United States)

    Kaine, B. P.; Mehr, I. J.; Woese, C. R.

    1994-01-01

    Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

  2. The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

    Science.gov (United States)

    Kaine, B. P.; Mehr, I. J.; Woese, C. R.

    1994-01-01

    Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

  3. BEYOND THE MAIN SEQUENCE: TESTING THE ACCURACY OF STELLAR MASSES PREDICTED BY THE PARSEC EVOLUTIONARY TRACKS

    Energy Technology Data Exchange (ETDEWEB)

    Ghezzi, Luan; Johnson, John Asher, E-mail: lghezzi@cfa.harvard.edu [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2015-10-20

    Characterizing the physical properties of exoplanets and understanding their formation and orbital evolution requires precise and accurate knowledge of their host stars. Accurately measuring stellar masses is particularly important because they likely influence planet occurrence and the architectures of planetary systems. Single main-sequence stars typically have masses estimated from evolutionary tracks, which generally provide accurate results due to their extensive empirical calibration. However, the validity of this method for subgiants and giants has been called into question by recent studies, with suggestions that the masses of these evolved stars could have been overestimated. We investigate these concerns using a sample of 59 benchmark evolved stars with model-independent masses (from binary systems or asteroseismology) obtained from the literature. We find very good agreement between these benchmark masses and the ones estimated using evolutionary tracks. The average fractional difference in the mass interval ∼0.7–4.5 M{sub ⊙} is consistent with zero (−1.30 ± 2.42%), with no significant trends in the residuals relative to the input parameters. A good agreement between model-dependent and -independent radii (−4.81 ± 1.32%) and surface gravities (0.71 ± 0.51%) is also found. The consistency between independently determined ages for members of binary systems adds further support for the accuracy of the method employed to derive the stellar masses. Taken together, our results indicate that determination of masses of evolved stars using grids of evolutionary tracks is not significantly affected by systematic errors, and is thus valid for estimating the masses of isolated stars beyond the main sequence.

  4. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference

    Directory of Open Access Journals (Sweden)

    Park Jongsun

    2008-01-01

    Full Text Available Abstract Background Simple sequence repeats (SSRs have been successfully used for various genetic and evolutionary studies in eukaryotic systems. The eukaryotic model organism Neurospora crassa is an excellent system to study evolution and biological function of SSRs. Results We identified and characterized 2749 SSRs of 963 SSR types in the genome of N. crassa. The distribution of tri-nucleotide (nt SSRs, the most common SSRs in N. crassa, was significantly biased in exons. We further characterized the distribution of 19 abundant SSR types (AST, which account for 71% of total SSRs in the N. crassa genome, using a Poisson log-linear model. We also characterized the size variation of SSRs among natural accessions using Polymorphic Index Content (PIC and ANOVA analyses and found that there are genome-wide, chromosome-dependent and local-specific variations. Using polymorphic SSRs, we have built linkage maps from three line-cross populations. Conclusion Taking our computational, statistical and experimental data together, we conclude that 1 the distributions of the SSRs in the sequenced N. crassa genome differ systematically between chromosomes as well as between SSR types, 2 the size variation of tri-nt SSRs in exons might be an important mechanism in generating functional variation of proteins in N. crassa, 3 there are different levels of evolutionary forces in variation of amino acid repeats, and 4 SSRs are stable molecular markers for genetic studies in N. crassa.

  5. White dwarf evolutionary sequences for low-metallicity progenitors: The impact of third dredge-up

    CERN Document Server

    Althaus, Leandro G; Bertolami, Marcelo M Miller; Córsico, Alejandro H; García-Berro, Enrique

    2015-01-01

    We present new white dwarf evolutionary sequences for low-metallicity progenitors. White dwarf sequences have been derived from full evolutionary calculations that take into account the entire history of progenitor stars, including the thermally-pulsing and the post-asymptotic giant branch phases. We show that for progenitor metallicities in the range 0.00003--0.001, and in the absence of carbon enrichment due to the occurrence of a third dredge-up episode, the resulting H envelope of the low-mass white dwarfs is thick enough to make stable H burning the most important energy source even at low luminosities. This has a significant impact on white dwarf cooling times. This result is independent of the adopted mass-loss rate during the thermally-pulsing and post-AGB phases, and the planetary nebulae stage. We conclude that in the absence of third dredge-up episodes, a significant part of the evolution of low-mass white dwarfs resulting from low-metallicity progenitors is dominated by stable H burning. Our study...

  6. Whole-genome sequencing of uropathogenic Escherichia coli reveals long evolutionary history of diversity and virulence.

    Science.gov (United States)

    Lo, Yancy; Zhang, Lixin; Foxman, Betsy; Zöllner, Sebastian

    2015-08-01

    Uropathogenic Escherichia coli (UPEC) are phenotypically and genotypically very diverse. This diversity makes it challenging to understand the evolution of UPEC adaptations responsible for causing urinary tract infections (UTI). To gain insight into the relationship between evolutionary divergence and adaptive paths to uropathogenicity, we sequenced at deep coverage (190×) the genomes of 19 E. coli strains from urinary tract infection patients from the same geographic area. Our sample consisted of 14 UPEC isolates and 5 non-UTI-causing (commensal) rectal E. coli isolates. After identifying strain variants using de novo assembly-based methods, we clustered the strains based on pairwise sequence differences using a neighbor-joining algorithm. We examined evolutionary signals on the whole-genome phylogeny and contrasted these signals with those found on gene trees constructed based on specific uropathogenic virulence factors. The whole-genome phylogeny showed that the divergence between UPEC and commensal E. coli strains without known UPEC virulence factors happened over 32 million generations ago. Pairwise diversity between any two strains was also high, suggesting multiple genetic origins of uropathogenic strains in a small geographic region. Contrasting the whole-genome phylogeny with three gene trees constructed from common uropathogenic virulence factors, we detected no selective advantage of these virulence genes over other genomic regions. These results suggest that UPEC acquired uropathogenicity long time ago and used it opportunistically to cause extraintestinal infections.

  7. Rotating Massive Main-Sequence Stars I: Grids of Evolutionary Models and Isochrones

    CERN Document Server

    Brott, Ines; Cantiello, Matteo; Langer, Norbert; de Koter, Alex; Evans, Chris J; Hunter, Ian; Trundle, Carrie; Vink, Jorick S

    2011-01-01

    We present a dense grid of evolutionary tracks and isochrones of rotating massive main-sequence stars. We provide three grids with different initial compositions tailored to compare with early OB stars in the Small and Large Magellanic Clouds and in the Galaxy. Each grid covers masses ranging from 5 to 60 Msun and initial rotation rates between 0 and about 600 km/s. To calibrate our models we used the results of the VLT-FLAMES Survey of Massive Stars. We determine the amount of convective overshooting by using the observed drop in rotation rates for stars with surface gravities log g < 3.2 to determine the width of the main sequence. We calibrate the efficiency of rotationally induced mixing using the nitrogen abundance determinations for B stars in the Large Magellanic cloud. We describe and provide evolutionary tracks and the evolution of the central and surface abundances. In particular, we discuss the occurrence of quasi-chemically homogeneous evolution, i.e. the severe effects of efficient mixing of t...

  8. Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.

    Science.gov (United States)

    Veidenberg, Andres; Medlar, Alan; Löytynoja, Ari

    2016-04-01

    Wasabi is an open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, and it can be easily extended with other tools. Along with drag-and-drop import of local files, Wasabi can access remote data through URL and import sequence data, GeneTrees and EPO alignments directly from Ensembl. To demonstrate a typical workflow using Wasabi, we reproduce key findings from recent comparative genomics studies, including a reanalysis of the EGLN1 gene from the tiger genome study: These case studies can be browsed within Wasabi at http://wasabiapp.org:8000?id=usecases. Wasabi runs inside a web browser and does not require any installation. One can start using it at http://wasabiapp.org. All source code is licensed under the AGPLv3.

  9. Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

    Directory of Open Access Journals (Sweden)

    Ruiz-Herrera Aurora

    2007-10-01

    Full Text Available Abstract Background Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria. Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results We described 29 fragile sites in the aardvark (OAF genome, 27 in the golden mole (CAS, and 35 in the elephant-shrew (EED genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion We provide evidence that (i the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared

  10. Reconstructing Networks from Profit Sequences in Evolutionary Games via a Multiobjective Optimization Approach with Lasso Initialization

    Science.gov (United States)

    Wu, Kai; Liu, Jing; Wang, Shuai

    2016-11-01

    Evolutionary games (EG) model a common type of interactions in various complex, networked, natural and social systems. Given such a system with only profit sequences being available, reconstructing the interacting structure of EG networks is fundamental to understand and control its collective dynamics. Existing approaches used to handle this problem, such as the lasso, a convex optimization method, need a user-defined constant to control the tradeoff between the natural sparsity of networks and measurement error (the difference between observed data and simulated data). However, a shortcoming of these approaches is that it is not easy to determine these key parameters which can maximize the performance. In contrast to these approaches, we first model the EG network reconstruction problem as a multiobjective optimization problem (MOP), and then develop a framework which involves multiobjective evolutionary algorithm (MOEA), followed by solution selection based on knee regions, termed as MOEANet, to solve this MOP. We also design an effective initialization operator based on the lasso for MOEA. We apply the proposed method to reconstruct various types of synthetic and real-world networks, and the results show that our approach is effective to avoid the above parameter selecting problem and can reconstruct EG networks with high accuracy.

  11. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

    Directory of Open Access Journals (Sweden)

    Lynch Michael

    2010-05-01

    Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  12. On the evolutionary status of chemically peculiar stars of the upper main sequence

    CERN Document Server

    Poehnl, H; Paunzen, E

    2003-01-01

    We present further evidence that the magnetic chemically peculiar stars (CP2) of the upper main sequence already occur at very early stages of the stellar evolution, significantly before they reach 30% of their life-time on the main sequence. This result is especially important for models dealing with dynamo theories, angular momentum loss during the pre- as well as main sequence and evolutionary calculations for CP2 stars. Results form the literature either derived for objects in the Hyades and the UMa cluster or from the Hipparcos mission contradict each other. A way out of this dilemma is to investigate young open clusters with known ages and accurate distances (error < 10%), including CP2 members. Up to now, four open clusters fulfill these requirements: IC 2391, IC 2602, NGC 2451A and NGC 2516. In total, 13 CP2 stars can be found within these clusters. We have used the measurements and calibrations of the Geneva 7-color photometric systems to derive effective temperatures and luminosities. Taking into...

  13. Whole Genome Sequencing Allows Better Understanding of the Evolutionary History of Leptospira interrogans Serovar Hardjo

    Science.gov (United States)

    Llanes, Alejandro; Restrepo, Carlos Mario; Rajeev, Sreekumari

    2016-01-01

    The genome of a laboratory-adapted strain of Leptospira interrogans serovar Hardjo was sequenced and analyzed. Comparison of the sequenced genome with that recently published for a field isolate of the same serovar revealed relatively high sequence conservation at the nucleotide level, despite the different biological background of both samples. Conversely, comparison of both serovar Hardjo genomes with those of L. borgpetersenii serovar Hardjo showed extensive differences between the corresponding chromosomes, except for the region occupied by their rfb loci. Additionally, comparison of the serovar Hardjo genomes with those of different L. interrogans serovars allowed us to detect several genomic features that may confer an adaptive advantage to L. interrogans serovar Hardjo, including a possible integrated plasmid and an additional copy of a cluster encoding a membrane transport system known to be involved in drug resistance. A phylogenomic strategy was used to better understand the evolutionary position of the Hardjo serovar among L. interrogans serovars and other Leptospira species. The proposed phylogeny supports the hypothesis that the presence of similar rfb loci in two different species may be the result of a lateral gene transfer event. PMID:27442015

  14. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  15. Evolutionary connections of biological kingdoms based on protein and nucleic acid sequence evidence

    Science.gov (United States)

    Dayhoff, M. O.

    1983-01-01

    Prokaryotic and eukaryotic evolutionary trees are developed from protein and nucleic-acid sequences by the methods of numerical taxonomy. Trees are presented for bacterial ferredoxins, 5S ribosomal RNA, c-type cytochromes , cytochromes c2 and c', and 5.8S ribosomal RNA; the implications for early evolution are discussed; and a composite tree showing the branching of the anaerobes, aerobes, archaebacteria, and eukaryotes is shown. Single lines are found for all oxygen-evolving photosynthetic forms and for the salt-loving and high-temperature forms of archaebacteria. It is argued that the eukaryote mitochondria, chloroplasts, and cytoplasmic host material are descended from free-living prokaryotes that formed symbiotic associations, with more than one symbiotic event involved in the evolution of each organelle.

  16. Cloning of two glutamate dehydrogenase cDNAs from Asparagus officinalis: sequence analysis and evolutionary implications.

    Science.gov (United States)

    Pavesi, A; Ficarelli, A; Tassi, F; Restivo, F M

    2000-04-01

    Two different amplification products, termed c1 and c2, showing a high similarity to glutamate dehydrogenase sequences from plants, were obtained from Asparagus officinalis using two degenerated primers and RT-PCR (reverse transcriptase polymerase chain reaction). The genes corresponding to these cDNA clones were designated aspGDHA and aspGDHB. Screening of a cDNA library resulted in the isolation of cDNA clones for aspGDHB only. Analysis of the deduced amino acid (aa) sequence from the full-length cDNA suggests that the gene product contains all regions associated with metabolic function of NAD glutamate dehydrogenase (NAD-GDH). A first phylogenetic analysis including only GDHs from plants suggested that the two GDH genes of A. officinalis arose by an ancient duplication event, pre-dating the divergence of monocots and dicots. Codon usage analysis showed a bias towards A/T ending codons. This tendency is likely due to the biased nucleotide composition of the asparagus genome, rather than to the translational selection for specific codons. Using principal coordinate analysis, the evolutionary relatedness of plant GDHs with homologous sequences from a large spectrum of organisms was investigated. The results showed a closer affinity of plant GDHs to GDHs of thermophilic archaebacterial and eubacterial species, when compared to those of unicellular eukaryotic fungi. Sequence analysis at specific amino acid signatures, known to affect the thermal stability of GDH, and assays of enzyme activity at non-physiological temperatures, showed a greater adaptation to heat-stress conditions for the asparagus and tobacco enzymes compared with the Saccharomyces cerevisiae enzyme.

  17. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

    Directory of Open Access Journals (Sweden)

    Ganko Eric W

    2004-03-01

    Full Text Available Abstract Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (

  18. Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences

    Directory of Open Access Journals (Sweden)

    Keiko Tanaka

    2013-01-01

    Full Text Available Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai. Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.

  19. Whole-Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements.

    Directory of Open Access Journals (Sweden)

    Kenneth A Stapleford

    2016-01-01

    Full Text Available Chikungunya virus (CHIKV, an alphavirus and member of the Togaviridae family, is capable of causing severe febrile disease in humans. In December of 2013 the Asian Lineage of CHIKV spread from the Old World to the Americas, spreading rapidly throughout the New World. Given this new emergence in naïve populations we studied the viral genetic diversity present in infected individuals to understand how CHIKV may have evolved during this continuing outbreak.We used deep-sequencing technologies coupled with well-established bioinformatics pipelines to characterize the minority variants and diversity present in CHIKV infected individuals from Guadeloupe and Martinique, two islands in the center of the epidemic. We observed changes in the consensus sequence as well as a diverse range of minority variants present at various levels in the population. Furthermore, we found that overall diversity was dramatically reduced after single passages in cell lines. Finally, we constructed an infectious clone from this outbreak and identified a novel 3' untranslated region (UTR structure, not previously found in nature, that led to increased replication in insect cells.Here we preformed an intrahost quasispecies analysis of the new CHIKV outbreak in the Caribbean. We identified novel variants present in infected individuals, as well as a new 3'UTR structure, suggesting that CHIKV has rapidly evolved in a short period of time once it entered this naïve population. These studies highlight the need to continue viral diversity surveillance over time as this epidemic evolves in order to understand the evolutionary potential of CHIKV.

  20. Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

    Directory of Open Access Journals (Sweden)

    Sanzo Miyazawa

    Full Text Available BACKGROUND: A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated. RESULTS: The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that

  1. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    Science.gov (United States)

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.

  2. An alternative hybrid evolutionary technique focused on allocating machines and sequencing operations

    Directory of Open Access Journals (Sweden)

    Mariano Frutos

    2016-09-01

    Full Text Available We present here a hybrid algorithm for the Flexible Job-Shop Scheduling Problem (FJSSP. This problem involves the optimal use of resources in a flexible production environment in which each operation can be carried out by more than a single machine. Our algorithm allocates, in a first step, the machines to operations and in a second stage it sequences them by integrating a Multi-Objective Evolutionary Algorithm (MOEA and a path-dependent search algorithm (Multi-Objective Simulated Annealing, which is enacted at the genetic phase of the procedure. The joint interaction of those two components yields a very efficient procedure for solving the FJSSP. An important step in the development of the algorithm was the selection of the right MOEA. Candidates were tested on problems of low, medium and high complexity. Further analyses showed the relevance of the search algorithm in the hybrid structure. Finally, comparisons with other algorithms in the literature indicate that the performance of our alternative is good.

  3. Synthetic observations of first hydrostatic cores in collapsing low-mass dense cores. I. Spectral energy distributions and evolutionary sequence

    CERN Document Server

    Commercon, Benoit; Dullemond, Cornelis P; Henning, Thomas

    2012-01-01

    The low-mass star formation evolutionary sequence is relatively well-defined both from observations and theoretical considerations. The first hydrostatic core is the first protostellar equilibrium object that is formed during the star formation process. Using state-of-the-art radiation-magneto-hydrodynamic 3D adaptive mesh refinement calculations, we aim to provide predictions for the dust continuum emission from first hydrostatic cores. We investigate the collapse and the fragmentation of magnetized one solar mass prestellar dense cores and the formation and evolution of first hydrostatic cores using the RAMSES code. We use three different magnetization levels for the initial conditions, which cover a large variety of early evolutionary morphology, e.g., the formation of a disk or a pseudo-disk, outflow launching, and fragmentation. We post-process the dynamical calculations using the 3D radiative transfer code RADMC-3D. We compute spectral energy distributions and usual evolutionary stage indicators such as...

  4. Pulsating low-mass white dwarfs in the frame of new evolutionary sequences. I. Adiabatic properties

    Science.gov (United States)

    Córsico, A. H.; Althaus, L. G.

    2014-09-01

    Context. Many low-mass white dwarfs with masses M∗/M⊙ ≲ 0.45, including the so-called extremely low-mass white dwarfs (M∗/M⊙ ≲ 0.20 - 0.25), have recently been discovered in the field of our Galaxy through dedicated photometric surveys. The subsequent discovery of pulsations in some of them has opened the unprecedented opportunity of probing the internal structure of these ancient stars. Aims: We present a detailed adiabatic pulsational study of these stars based on full evolutionary sequences derived from binary star evolution computations. The main aim of this study is to provide a detailed theoretical basis of reference for interpreting present and future observations of variable low-mass white dwarfs. Methods: Our pulsational analysis is based on a new set of He-core white-dwarf models with masses ranging from 0.1554 to 0.4352 M⊙ derived by computing the non-conservative evolution of a binary system consisting of an initially 1 M⊙ ZAMS star and a 1.4 M⊙ neutron star. We computed adiabatic radial (ℓ = 0) and non-radial (ℓ = 1,2) p and g modes to assess the dependence of the pulsational properties of these objects on stellar parameters such as the stellar mass and the effective temperature, as well as the effects of element diffusion. Results: We found that for white dwarf models with masses below ~ 0.18 M⊙, g modes mainly probe the core regions and p modes the envelope, therefore pulsations offer the opportunity of constraining both the core and envelope chemical structure of these stars via asteroseismology. For models with M∗ ≳ 0.18 M⊙, on the other hand, g modes are very sensitive to the He/H compositional gradient and therefore can be used as a diagnostic tool for constraining the H envelope thickness. Because both types of objects have not only very distinct evolutionary histories (according to whether the progenitor stars have experienced CNO-flashes or not), but also have strongly different pulsation properties, we propose to

  5. Synthetic observations of first hydrostatic cores in collapsing low-mass dense cores. I. Spectral energy distributions and evolutionary sequence

    OpenAIRE

    Commercon, Benoit; Launhardt, Ralf; Dullemond, Cornelis P.; Henning, Thomas

    2012-01-01

    The low-mass star formation evolutionary sequence is relatively well-defined both from observations and theoretical considerations. The first hydrostatic core is the first protostellar equilibrium object that is formed during the star formation process. Using state-of-the-art radiation-magneto-hydrodynamic 3D adaptive mesh refinement calculations, we aim to provide predictions for the dust continuum emission from first hydrostatic cores. We investigate the collapse and the fragmentation of ma...

  6. Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes.

    Science.gov (United States)

    Ruiz-Dueñas, Francisco J; Lundell, Taina; Floudas, Dimitrios; Nagy, Laszlo G; Barrasa, José M; Hibbett, David S; Martínez, Angel T

    2013-01-01

    The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species representing the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequenced B. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)-oxidation site being at the origin of all the LiP enzymes, which are found only in

  7. Synthetic observations of first hydrostatic cores in collapsing low-mass dense cores. I. Spectral energy distributions and evolutionary sequence

    Science.gov (United States)

    Commerçon, B.; Launhardt, R.; Dullemond, C.; Henning, Th.

    2012-09-01

    Context. The low-mass star formation evolutionary sequence is relatively well-defined both from observations and theoretical considerations. The first hydrostatic core is the first protostellar equilibrium object that is formed during the star formation process. Aims: Using state-of-the-art radiation-magneto-hydrodynamic 3D adaptive mesh refinement calculations, we aim to provide predictions for the dust continuum emission from first hydrostatic cores. Methods: We investigated the collapse and the fragmentation of magnetized 1 M⊙ prestellar dense cores and the formation and evolution of first hydrostatic cores using the RAMSES code. We used three different magnetization levels for the initial conditions, which cover a wide variety of early evolutionary morphology, e.g., the formation of a disk or a pseudo-disk, outflow launching, and fragmentation. We post-processed the dynamical calculations using the 3D radiative transfer code RADMC-3D. We computed spectral energy distributions and usual evolutionary stage indicators such as bolometric luminosity and temperature. Results: We find that the first hydrostatic core lifetimes depend strongly on the initial magnetization level of the parent dense core. We derive, for the first time, spectral energy distribution evolutionary sequences from high-resolution radiation-magneto-hydrodynamic calculations. We show that under certain conditions, first hydrostatic cores can be identified from dust continuum emission at 24 μm and 70 μm. We also show that single spectral energy distributions cannot help in distinguishing between the formation scenarios of the first hydrostatic core, i.e., between the magnetized and non-magnetized models. Conclusions: Spectral energy distributions are a first useful and direct way to target first hydrostatic core candidates but high-resolution interferometry is definitively needed to determine the evolutionary stage of the observed sources.

  8. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

    Directory of Open Access Journals (Sweden)

    Jiaqin Shi

    Full Text Available Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences. The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type the angiosperm species (aside from a few species all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite

  9. Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code.

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    Feng-Jie Sun

    Full Text Available Transfer RNA (tRNA molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.

  10. The Gaia-ESO Survey: the first abundance determination of the pre-main-sequence cluster Gamma Velorum

    CERN Document Server

    Spina, L; Palla, F; Sacco, G G; Magrini, L; Franciosini, E; Morbidelli, L; Prisinzano, L; Alfaro, E J; Biazzo, K; Frasca, A; Hernandez, J I Gonzalez; Sousa, S G; Adibekyan, V; Delgado-Mena, E; Montes, D; Tabernero, H; Klutsch, A; Gilmore, G; Feltzing, S; Jeffries, R D; Micela, G; Vallenari, A; Bensby, T; Bragaglia, A; Flaccomio, E; Koposov, S; Lanzafame, A C; Pancino, E; Recio-Blanco, A; Smiljanic, R; Costado, M T; Damiani, F; Hill, V; Hourihane, A; Jofre, P; de Laverny, P; Masseron, T; Worley, C

    2014-01-01

    Knowledge of the abundance distribution of star forming regions and young clusters is critical to investigate a variety of issues, from triggered star formation and chemical enrichment by nearby supernova explosions to the ability to form planetary systems.In spite of this, detailed abundance studies are currently available for relatively few regions. In this context, we present the analysis of the metallicity of the Gamma Velorum cluster, based on the products distributed in the first internal release of the Gaia-ESO Survey. The Gamma Velorum candidate members have been observed with FLAMES, using both UVES and Giraffe, depending on the target brightness and spectral type. In order to derive a solid metallicity determination for the cluster, membership of the observed stars must be first assessed. To this aim, we use several membership criteria including radial velocities, surface gravity estimates, and the detection of the photospheric lithium line. Out of the 80 targets observed with UVES, we identify 14 h...

  11. The Gaia-ESO Survey: pre-main-sequence stars in the young open cluster NGC 3293

    Science.gov (United States)

    Delgado, A. J.; Sampedro, L.; Alfaro, E. J.; Costado, M. T.; Yun, J. L.; Frasca, A.; Lanzafame, A. C.; Drew, J. E.; Eislöffel, J.; Blomme, R.; Morel, T.; Lobel, A.; Semaan, T.; Randich, S.; Jeffries, R. D.; Micela, G.; Vallenari, A.; Kalari, V.; Gilmore, G.; Flaccomio, E.; Carraro, G.; Lardo, C.; Monaco, L.; Prisinzano, L.; Sousa, S. G.; Morbidelli, L.; Lewis, J.; Koposov, S.; Hourihane, A.; Worley, C.; Casey, A.; Franciosini, E.; Sacco, G.; Magrini, L.

    2016-08-01

    The young open cluster NGC3293 is included in the observing program of the Gaia-ESO survey (GES). The radial velocity values provided have been used to assign cluster membership probabilities by means of a single-variable parametric analysis. These membership probabilities are compared to the results of the photometric membership assignment of NGC3293, based on UBVRI photometry. The agreement of the photometric and kinematic member samples amounts to 65 per cent, and could increase to 70 per cent as suggested by the analysis of the differences between both samples. A number of photometric PMS candidate members of spectral type F are found, which are confirmed by the results from VPHAS photometry and SED fitting for the stars in common with VPHAS and GES data sets. Excesses at mid- and near-infrared wavelengths, and signs of Hα emission, are investigated for them. Marginal presence of Hα emission or infilling is detected for the candidate members. Several of them exhibit moderate signs of U excess and weak excesses at mid-IR wavelengths. We suggest that these features originate from accretion discs in their last stages of evolution.

  12. Dust disks around old Pre Main-Sequence stars HST\\/NICMOS2 scattered light images and modeling

    CERN Document Server

    Augereau, J C; Mouillet, D; Ménard, F

    2000-01-01

    We present recent near-infrared detections of circumstellar disks around the two old PMS Herbig stars HD 141569 and HD 100546 obtained with the HST/NICMOS2 camera. They reveal extended structures larger than 350-400 AU in radius. While the HD 100546 disk appears as a continuous disk down to 40 AU, the HD 141569 environment seems more complex, splitted at least into two dust populations. As a convincing example, the full modeling of the disk surrounding HR 4796, another old PMS star, is detailed and confronted with more recent observations.

  13. EXPORT : Spectral classification and projected rotational velocities of Vega-type and pre-main sequence stars

    NARCIS (Netherlands)

    Mora, A; Merin, B; Solano, E; Montesinos, B; de Winter, D; Eiroa, C; Ferlet, R; Grady, CA; Miranda, LF; Oudmaijer, RD; Palacios, J; Quirrenbach, A; Harris, AW; Rauer, H; Cameron, A; Deeg, HJ; Garzon, F; Penny, A; Schneider, J; Tsapras, Y; Wesselius, PR

    2001-01-01

    In this paper we present the first comprehensive results extracted from the spectroscopic campaigns carried out by the EXPORT (EXoPlanetary Observational Research Team) consortium. During 1998-1999, EXPORT carried out an intensive observational effort in the framework of the origin and evolution of

  14. The fate of the pre-main sequence-rich clusters Collinder197 and vdB92: dissolution?

    CERN Document Server

    Bonatto, Charles

    2010-01-01

    We investigate the nature and possible evolution of the young Galactic star clusters Collinder 197 (Cr 197) and vdB 92. The colour-magnitude diagrams (CMDs) are basically characterised by a poorly-populated MS and a dominant fraction ($\\ga75%$) of PMS stars, and the combined MS and PMS CMD morphology in both clusters consistently constrains the age to within $5\\pm4$ Myr, with a $\\sim10$ Myr spread in the star formation process. The MS$ + $PMS stellar masses are $\\approx660^{+102}_{-59} \\ms$ (Cr 197) and $\\approx750^{+101}_{-51} \\ms$ (vdB 92). Cr 197 and vdB 92 appear to be abnormally large, when compared to clusters within the same age range. They have irregular stellar radial density distributions (RDPs) with a marked excess in the innermost region, a feature that, at less than 10 Myr, is more likely related to the star formation and/or molecular cloud fragmentation than to age-dependent dynamical effects. The velocity dispersion of both clusters, derived from proper motions, is in the range $\\sim15 - 22 \\km...

  15. Accretion and outflow activity on the late phases of pre-main-sequence evolution. The case of RZ Piscium

    Science.gov (United States)

    Potravnov, I. S.; Mkrtichian, D. E.; Grinin, V. P.; Ilyin, I. V.; Shakhovskoy, D. N.

    2017-03-01

    RZ Psc is an isolated high-latitude post-T Tauri star that demonstrates a UX Ori-type photometric activity. The star shows very weak spectroscopic signatures of accretion, but at the same time possesses the unusual footprints of the wind in Na i D lines. In the present work we investigate new spectroscopic observations of RZ Psc obtained in 2014 during two observation runs. We found variable blueshifted absorption components (BACs) in lines of the other alcali metals, K i 7699 Å and Ca ii IR triplet. We also confirmed the presence of a weak emission component in the Hα line, which allowed us to estimate the mass accretion rate on the star as Ṁ ≤ 7 × 10-12M⊙ yr-1. We could not reveal any clear periodicity in the appearance of BACs in sodium lines. Nevertheless, the exact coincidence of the structure and velocities of the Na i D absorptions observed with the interval of about one year suggests that such a periodicity should exist.

  16. Stellar Activity on the Young Suns of Orion: COUP Observations of K5-7 Pre-Main Sequence Stars

    CERN Document Server

    Wolk, S J; Micela, G; Favata, F; Glassgold, A E; Shang, H; Feigelson, E D

    2005-01-01

    In January 2003, the Chandra Orion Ultradeep Project (COUP) detected about 1400 young stars during a 13.2 day observation of the Orion Nebula Cluster (ONC). This paper studies a well-defined sample of 28 solar-mass COUP sources to characterize the magnetic activity of analogs of the young Sun and thereby to improve understanding of the effects of solar X-rays on the solar nebula during the era of planet formation. We find that active young Suns spend 70% of their time in a characteristic state with relatively constant flux and magnetically confined plasma with temperatures kT_2 = 2.1 * kT_1. During characteristic periods, the 0.5-8 keV X-ray luminosity is about 0.03% of the bolometric luminosity. One or two powerful flares per week with peak luminosities logL_x ~ 30-32 erg/s are typically superposed on this characteristic emission accompanied by heating of the hot plasma component from ~2.4 keV to ~7 keV at the flare peak. The energy distribution of flares superposed on the characteristic emission level follo...

  17. Long-term BVRI light curves of 5 pre-main sequence stars in the field of "Gulf of Mexico"

    CERN Document Server

    Ibryamov, Sunay I; Peneva, Stoyanka P

    2014-01-01

    We present new data from BVRI photometric observations of five PMS stars during the period from April 2013 to July 2014. The stars are located in the field of NGC 7000/IC 5070 ("Gulf of Mexico") - a region with active star formation. The presented paper is a continuation of our long-term photometric investigations of the young stellar objects in this region. The long-term multicolor photometric observations of PMS stars are very important for their exact classification. Our results show that the studied stars exhibit different types of photometric variability in all bands. We tried to classify them using our data from the long-term photometry and data published by other authors.

  18. Long-term BVRI light curves of 5 pre-main sequence stars in the field of "Gulf of Mexico"

    OpenAIRE

    Ibryamov, Sunay I.; Semkov, Evgeni H.; Peneva, Stoyanka P.

    2014-01-01

    We present new data from BVRI photometric observations of five PMS stars during the period from April 2013 to July 2014. The stars are located in the field of NGC 7000/IC 5070 ("Gulf of Mexico") - a region with active star formation. The presented paper is a continuation of our long-term photometric investigations of the young stellar objects in this region. The long-term multicolor photometric observations of PMS stars are very important for their exact classification. Our results show that ...

  19. New evolutionary sequences for hot H-deficient white dwarfs on the basis of a full account of progenitor evolution

    CERN Document Server

    Althaus, L G; Bertolami, M M Miller; García-Berro, E; Córsico, A H; Romero, A D; Kepler, S O; Rohrmann, R D

    2009-01-01

    We present full evolutionary calculations appropriate for the study of hot hydrogen-deficent DO white dwarfs, PG 1159 stars, and DB white dwarfs. White dwarf sequences are computed for a wide range of stellar masses and helium envelopes on the basis of a complete treatment of the evolutionary history of progenitors stars, including the core hydrogen and helium burning phases, the thermally-pulsing AGB phase, and the born-again episode that is responsible for the hydrogen deficiency. We also provide colors and magnitudes for the new sequences for $T_{\\rm eff} < 40 000$ K, where the NLTE effects are not dominant. These new calculations provide an homogeneous set of evolutionary tracks appropriate for mass and age determinations for both PG 1159 stars and DO white dwarfs. The calculations are extended down to an effective temperature of 7 000 K. We applied these new tracks to redetermine stellar masses and ages of all known DO white dwarfs with spectroscopically-determined effective temperatures and gravities...

  20. Extensive sequence turnover of the signal peptides of members of the GDF/BMP family: exploring their evolutionary landscape

    Directory of Open Access Journals (Sweden)

    Veitia Reiner A

    2009-07-01

    Full Text Available Abstract We show that the predicted signal peptide (SP sequences of the secreted factors GDF9, BMP15 and AMH are well conserved in mammals but dramatic divergence is noticed for more distant orthologs. Interestingly, bioinformatic predictions show that the divergent protein segments do encode SPs. Thus, such SPs have undergone extensive sequence turnover with full preservation of functionality. This can be explained by a pervasive accumulation of neutral and compensatory mutations. An exploration of the potential evolutionary landscape of some SPs is presented. Some of these signal sequences highlight an apparent paradox: they are encoded, by definition, by orthologous DNA segments but they are, given their striking divergence, examples of what can be called functional convergence. Reviewers: This article was reviewed by Fyodor Kondrashov and Eugene V. Koonin.

  1. Cloning and sequencing analysis of three amylase cDNAs in the shrimp Penaeus vannamei (Crustacea decapoda): evolutionary aspects.

    Science.gov (United States)

    Van Wormhoudt, A; Sellos, D

    1996-05-01

    In Penaeus vannamei, alpha-amylase is the most important glucosidase and is present as at least two major isoenzymes which have been purified. In order to obtain information on their structure, a hepatopancreas cDNA library constructed in phage lambda-Zap II (Strategene) was screened using a synthetic oligonucleotide based on the amino acid sequence of a V8 staphylococcal protease peptide of P. vannamei alpha-amylase. Three clones were selected: AMY SK 37 (EMBL sequence accession number: X 77318) is the most complete of the analyzed clones and was completely sequenced. It contains the complete cDNA sequence coding for one of the major isoenzymes of shrimp amylase. The deduced amino acid sequence shows the existence of a 511-residue-long pre-enzyme containing a highly hydrophobic signal peptide of 16 amino acids. Northern hybridization of total RNA with the amylase cDNA confirms the size of the messenger at around 1,600 bases. AMY SK 28, which contains the complete mature sequence of amylase, belonged to the same family characterized by a common 3' terminus and presented four amino acid changes. Some other variants of this family were also partially sequenced. AMY SK 20 was found to encode a minor variant of the protein with a different 3' terminus and 57 amino acid changes. Phylogenetic analysis established with the conserved amino acid regions of the (beta/alpha) eight-barrel domain and with the total sequence of P. vannamei showed close evolutionary relationships with mammals (59-63% identity) and with insect alpha-amylase (52-62% identity). The use of conserved sequences increased the level of similarity but it did not alter the ordering of the groupings. Location of the secondary structure elements confirmed the high level of sequence similarity of shrimp alpha-amylase with pig alpha-amylase.

  2. Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010.

    Directory of Open Access Journals (Sweden)

    Cecilia Rebuffo-Scheer

    Full Text Available BACKGROUND: Respiratory Syncytial Virus (RSV is the leading cause of lower respiratory-tract infections in infants and young children worldwide. Despite this, only six complete genome sequences of original strains have been previously published, the most recent of which dates back 35 and 26 years for RSV group A and group B respectively. METHODOLOGY/PRINCIPAL FINDINGS: We present a semi-automated sequencing method allowing for the sequencing of four RSV whole genomes simultaneously. We were able to sequence the complete coding sequences of 13 RSV A and 4 RSV B strains from Milwaukee collected from 1998-2010. Another 12 RSV A and 5 RSV B strains sequenced in this study cover the majority of the genome. All RSV A and RSV B sequences were analyzed by neighbor-joining, maximum parsimony and Bayesian phylogeny methods. Genetic diversity was high among RSV A viruses in Milwaukee including the circulation of multiple genotypes (GA1, GA2, GA5, GA7 with GA2 persisting throughout the 13 years of the study. However, RSV B genomes showed little variation with all belonging to the BA genotype. For RSV A, the same evolutionary patterns and clades were seen consistently across the whole genome including all intergenic, coding, and non-coding regions sequences. CONCLUSIONS/SIGNIFICANCE: The sequencing strategy presented in this work allows for RSV A and B genomes to be sequenced simultaneously in two working days and with a low cost. We have significantly increased the amount of genomic data that is available for both RSV A and B, providing the basic molecular characteristics of RSV strains circulating in Milwaukee over the last 13 years. This information can be used for comparative analysis with strains circulating in other communities around the world which should also help with the development of new strategies for control of RSV, specifically vaccine development and improvement of RSV diagnostics.

  3. New evolutionary sequences for extremely low mass white dwarfs: Homogeneous mass and age determinations, and asteroseismic prospects

    CERN Document Server

    Althaus, Leandro G; Córsico, Alejandro H

    2013-01-01

    We provide a fine and homogeneous grid of evolutionary sequences for He-core white dwarfs with masses 0.15-0.45 Msun, including the mass range for ELM white dwarfs (<0.20Msun). The grid is appropriate for mass and age determination, and to study their pulsational properties. White dwarf sequences have been computed by performing full evolutionary calculations that consider the main energy sources and processes of chemical abundance changes during white dwarf evolution. Initial models for the evolving white dwarfs have been obtained by computing the non-conservative evolution of a binary system consisting of a Msun ZAMS star and a 1.4 Msun neutron star for various initial orbital periods. To derive cooling ages and masses for He-core white dwarf we perform a least square fitting of the M(Teff, g) and Age(Teff, g) relations provided by our sequences by using a scheme that takes into account the time spent by models in different regions of the Teff-g plane. This is useful when multiple solutions for cooling a...

  4. MySSP: non-stationary evolutionary sequence simulation, including indels.

    Science.gov (United States)

    Rosenberg, Michael S

    2007-02-26

    MySSP is a new program for the simulation of DNA sequence evolution across a phylogenetic tree. Although many programs are available for sequence simulation, MySSP is unique in its inclusion of indels, flexibility in allowing for non-stationary patterns, and output of ancestral sequences. Some of these features can individually be found in existing programs, but have not all have been previously available in a single package.

  5. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.

    Science.gov (United States)

    Jehl, Peter; Manguy, Jean; Shields, Denis C; Higgins, Desmond G; Davey, Norman E

    2016-07-01

    Low-throughput experiments and high-throughput proteomic and genomic analyses have created enormous quantities of data that can be used to explore protein function and evolution. The ability to consolidate these data into an informative and intuitive format is vital to our capacity to comprehend these distinct but complementary sources of information. However, existing tools to visualize protein-related data are restricted by their presentation, sources of information, functionality or accessibility. We introduce ProViz, a powerful browser-based tool to aid biologists in building hypotheses and designing experiments by simplifying the analysis of functional and evolutionary features of proteins. Feature information is retrieved in an automated manner from resources describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterization of functional regions. These features are mapped to evolutionary information from precomputed multiple sequence alignments. Data are displayed in an interactive and information-rich yet intuitive visualization, accessible through a simple protein search interface. This allows users with limited bioinformatic skills to rapidly access data pertinent to their research. Visualizations can be further customized with user-defined data either manually or using a REST API. ProViz is available at http://proviz.ucd.ie/.

  6. Evolutionary status of isolated B[e] stars

    CERN Document Server

    Lee, Chien-De; Liu, S Y

    2016-01-01

    Aims. We study a sample of eight B[e] stars with uncertain evolutionary status to shed light on the origin of their circumstellar dust. Methods. We performed a diagnostic analysis on the spectral energy distribution beyond infrared wavelengths, and conducted a census of neighboring region of each target to ascertain its evolutionary status. Results. In comparison to pre-main sequence Herbig stars, these B[e] stars show equally substantial excess emission in the near-infrared, indicative of existence of warm dust, but much reduced excess at longer wavelengths, so the dusty envelopes should be compact in size. Isolation from star-forming regions excludes the possibility of their pre-main sequence status. Six of our targets, including HD 50138, HD 45677, CD-245721, CD-49 3441, MWC 623, and HD 85567, have been previously considered as FS CMa stars, whereas HD 181615/6 and HD 98922 are added to the sample by this work. We argue that the circumstellar grains of these isolated B[e] stars, already evolved beyond the ...

  7. Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs

    Directory of Open Access Journals (Sweden)

    Braasch Ingo

    2008-02-01

    Full Text Available Abstract Background The cichlid fishes in general, and the exceptionally diverse East African haplochromine cichlids in particular, are famous examples of adaptive radiation and explosive speciation. Here we report the collection and annotation of more than 12,000 expressed sequence tags (ESTs generated from three different cDNA libraries obtained from the East African haplochromine cichlid species Astatotilapia burtoni and Metriaclima zebra. Results We first annotated more than 12,000 newly generated cichlid ESTs using the Gene Ontology classification system. For evolutionary analyses, we combined these ESTs with all available sequence data for haplochromine cichlids, which resulted in a total of more than 45,000 ESTs. The ESTs represent a broad range of molecular functions and biological processes. We compared the haplochromine ESTs to sequence data from those available for other fish model systems such as pufferfish (Takifugu rubripes and Tetraodon nigroviridis, trout, and zebrafish. We characterized genes that show a faster or slower rate of base substitutions in haplochromine cichlids compared to other fish species, as this is indicative of a relaxed or reinforced selection regime. Four of these genes showed the signature of positive selection as revealed by calculating Ka/Ks ratios. Conclusion About 22% of the surveyed ESTs were found to have cichlid specific rate differences suggesting that these genes might play a role in lineage specific characteristics of cichlids. We also conclude that the four genes with a Ka/Ks ratio greater than one appear as good candidate genes for further work on the genetic basis of evolutionary success of haplochromine cichlid fishes.

  8. Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou's pseudo amino acid composition.

    Science.gov (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang

    2014-08-21

    Knowledge of protein structural class plays an important role in characterizing the overall folding type of a given protein. At present, it is still a challenge to extract sequence information solely using protein sequence for protein structural class prediction with low similarity sequence in the current computational biology. In this study, a novel sequence representation method is proposed based on position specific scoring matrix for protein structural class prediction. By defined evolutionary difference formula, varying length proteins are expressed as uniform dimensional vectors, which can represent evolutionary difference information between the adjacent residues of a given protein. To perform and evaluate the proposed method, support vector machine and jackknife tests are employed on three widely used datasets, 25PDB, 1189 and 640 datasets with sequence similarity lower than 25%, 40% and 25%, respectively. Comparison of our results with the previous methods shows that our method may provide a promising method to predict protein structural class especially for low-similarity sequences.

  9. New evolutionary tracks of massive stars with PARSEC

    Science.gov (United States)

    Chen, Yang; Bressan, Alessandro; Girardi, Leo; Marigo, Paola

    2015-08-01

    We present new evolutionary tracks of massive stars that complement the already published PARSEC database and supersede the old Padova evolutionary tracks of massive stars, which are more than 20 years old. We consider a broad range of metallicities, from Z=0.0001 to Z=0.04, and initial masses up to M=350 M⊙. The evolution is computed from the pre-main sequence phase up to the central carbon ignition. We supplement the new tracks with new tables of theoretical bolometric corrections in several photometric systems, obtained by homogenizing stellar atmosphere models of hot and cool stars, PoWR, WM-basic, ATLAS9 and Phoenix.The mass, age and metallicity grids are fully adequate to perform detailed investigations of the properties of very young stellar systems, in local and distant galaxies.

  10. A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus: an evolutionary history of camelidae

    Directory of Open Access Journals (Sweden)

    Meng He

    2007-07-01

    Full Text Available Abstract Background The family Camelidae that evolved in North America during the Eocene survived with two distinct tribes, Camelini and Lamini. To investigate the evolutionary relationship between them and to further understand the evolutionary history of this family, we determined the complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus, the only wild survivor of the Old World camel. Results The mitochondrial genome sequence (16,680 bp from C. bactrianus ferus contains 13 protein-coding, two rRNA, and 22 tRNA genes as well as a typical control region; this basic structure is shared by all metazoan mitochondrial genomes. Its protein-coding region exhibits codon usage common to all mammals and possesses the three cryptic stop codons shared by all vertebrates. C. bactrianus ferus together with the rest of mammalian species do not share a triplet nucleotide insertion (GCC that encodes a proline residue found only in the nd1 gene of the New World camelid Lama pacos. This lineage-specific insertion in the L. pacos mtDNA occurred after the split between the Old and New World camelids suggests that it may have functional implication since a proline insertion in a protein backbone usually alters protein conformation significantly, and nd1 gene has not been seen as polymorphic as the rest of ND family genes among camelids. Our phylogenetic study based on complete mitochondrial genomes excluding the control region suggested that the divergence of the two tribes may occur in the early Miocene; it is much earlier than what was deduced from the fossil record (11 million years. An evolutionary history reconstructed for the family Camelidae based on cytb sequences suggested that the split of bactrian camel and dromedary may have occurred in North America before the tribe Camelini migrated from North America to Asia. Conclusion Molecular clock analysis of complete mitochondrial genomes from C. bactrianus ferus and L

  11. Serine protease isoforms in Gloydius intermedius venom: Full sequences, molecular phylogeny and evolutionary implications.

    Science.gov (United States)

    Yang, Zhang-Min; Yu, Hui; Liu, Zhen-Zhen; Pei, Jian-Zhu; Yang, Yu-E; Yan, Su-Xian; Zhang, Cui; Zhao, Wen-Long; Wang, Zhe-Zhi; Wang, Ying-Ming; Tsai, Inn-Ho

    2017-07-05

    Nine distinct venom serine proteases (vSPs) of Gloydius intermedius were studied by transcriptomic, sub-proteomic and phylogenetic analyses. Their complete amino acid sequences were deduced after Expression Sequence Tag (EST) analyses followed by cDNA cloning and sequencing. These vSPs appear to be paralogs and contain the catalytic triads and 1-4 potential N-glycosylation sites. Their relative expression levels evaluated by qPCR were grossly consistent with their EST hit-numbers. The major vSPs were purified by HPLC and their N-terminal sequences matched well to the deduced sequences, while fragments of the minor vSPs were detected by LC-MS/MS identification. Specific amidolytic activities of the fractions from HPLC and anion exchange separation were assayed using four chromogenic substrates, respectively. Molecular phylogenetic tree based on the sequences of these vSPs and their orthologs revealed six major clusters, one of them covered four lineages of plasminogen activator like vSPs. N-glycosylation patterns and variations for the vSPs are discussed. The high sequence similarities between G. intermedius vSPs and their respective orthologs from American pitvipers suggest that most of the isoforms evolved before Asian pitvipers migrated to the New World. Our results also indicate that the neurotoxic venoms contain more kallikrein-like vSPs and hypotensive components than the hemorrhagic venoms. Full sequences and expression levels of nine paralogous serine proteases (designated as GiSPs) of Gloydius intermedius venom have been studied. A kallikrein-like enzyme is most abundant and four isoforms homologous to venom plasminogen-activators are also expressed in this venom. Taken together, the present and previous data demonstrate that the neurotoxic G. intermedius venoms contain more hypotensive vSPs relative to other hemorrhagic pitviper venoms and the pitviper vSPs are highly versatile and diverse. Their structure-function relationships remain to be explored and

  12. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

    Directory of Open Access Journals (Sweden)

    Olivier Arnaiz

    Full Text Available Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a

  13. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

    Science.gov (United States)

    Arnaiz, Olivier; Mathy, Nathalie; Baudry, Céline; Malinsky, Sophie; Aury, Jean-Marc; Denby Wilkes, Cyril; Garnier, Olivier; Labadie, Karine; Lauderdale, Benjamin E; Le Mouël, Anne; Marmignon, Antoine; Nowacki, Mariusz; Poulain, Julie; Prajer, Malgorzata; Wincker, Patrick; Meyer, Eric; Duharcourt, Sandra; Duret, Laurent; Bétermier, Mireille; Sperling, Linda

    2012-01-01

    Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the

  14. Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses

    Directory of Open Access Journals (Sweden)

    Igor R. Costa

    2014-12-01

    Full Text Available Essential amino acids (EAA consist of a group of nine amino acids that animals are unable to synthesize via de novo pathways. Recently, it has been found that most metazoans lack the same set of enzymes responsible for the de novo EAA biosynthesis. Here we investigate the sequence conservation and evolution of all the metazoan remaining genes for EAA pathways. Initially, the set of all 49 enzymes responsible for the EAA de novo biosynthesis in yeast was retrieved. These enzymes were used as BLAST queries to search for similar sequences in a database containing 10 complete metazoan genomes. Eight enzymes typically attributed to EAA pathways were found to be ubiquitous in metazoan genomes, suggesting a conserved functional role. In this study, we address the question of how these genes evolved after losing their pathway partners. To do this, we compared metazoan genes with their fungal and plant orthologs. Using phylogenetic analysis with maximum likelihood, we found that acetolactate synthase (ALS and betaine-homocysteine S-methyltransferase (BHMT diverged from the expected Tree of Life (ToL relationships. High sequence conservation in the paraphyletic group Plant-Fungi was identified for these two genes using a newly developed Python algorithm. Selective pressure analysis of ALS and BHMT protein sequences showed higher non-synonymous mutation ratios in comparisons between metazoans/fungi and metazoans/plants, supporting the hypothesis that these two genes have undergone non-ToL evolution in animals.

  15. Evidence of evolutionary constraints that influences the sequence composition and diversity of mitochondrial matrix targeting signals.

    Directory of Open Access Journals (Sweden)

    Stephen R Doyle

    Full Text Available Mitochondrial targeting signals (MTSs are responsible for trafficking nuclear encoded proteins to their final destination within mitochondria. These sequences are diverse, sharing little amino acid homology and vary significantly in length, and although the formation of a positively-charged amphiphilic alpha helix within the MTS is considered to be necessary and sufficient to mediate import, such a feature does not explain their diversity, nor how such diversity influences target sequence function, nor how such dissimilar signals interact with a single, evolutionarily conserved import mechanism. An in silico analysis of 296 N-terminal, matrix destined MTSs from Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis thaliana, and Oryza sativa was undertaken to investigate relationships between MTSs, and/or, relationships between an individual targeting signal sequence and the protein that it imports. We present evidence that suggests MTS diversity is influenced in part by physiochemical and N-terminal characteristics of their mature sequences, and that some of these correlated characteristics are evolutionarily maintained across a number of taxa. Importantly, some of these associations begin to explain the variation in MTS length and composition.

  16. Internalin profiling and multilocus sequence typing suggest four Listeria innocua subgroups with different evolutionary distances from Listeria monocytogenes

    Directory of Open Access Journals (Sweden)

    Wang Jun

    2010-03-01

    Full Text Available Abstract Background Ecological, biochemical and genetic resemblance as well as clear differences of virulence between L. monocytogenes and L. innocua make this bacterial clade attractive as a model to examine evolution of pathogenicity. This study was attempted to examine the population structure of L. innocua and the microevolution in the L. innocua-L. monocytogenes clade via profiling of 37 internalin genes and multilocus sequence typing based on the sequences of 9 unlinked genes gyrB, sigB, dapE, hisJ, ribC, purM, gap, tuf and betL. Results L. innocua was genetically monophyletic compared to L. monocytogenes, and comprised four subgroups. Subgroups A and B correlated with internalin types 1 and 3 (except the strain 0063 belonging to subgroup C and internalin types 2 and 4 respectively. The majority of L. innocua strains belonged to these two subgroups. Subgroup A harbored a whole set of L. monocytogenes-L. innocua common and L. innocua-specific internalin genes, and displayed higher recombination rates than those of subgroup B, including the relative frequency of occurrence of recombination versus mutation (ρ/θ and the relative effect of recombination versus point mutation (r/m. Subgroup A also exhibited a significantly smaller exterior/interior branch length ratio than expected under the coalescent model, suggesting a recent expansion of its population size. The phylogram based on the analysis with correction for recombination revealed that the time to the most recent common ancestor (TMRCA of L. innocua subgroups A and B were similar. Additionally, subgroup D, which correlated with internalin type 5, branched off from the other three subgroups. All L. innocua strains lacked seventeen virulence genes found in L. monocytogenes (except for the subgroup D strain L43 harboring inlJ and two subgroup B strains bearing bsh and were nonpathogenic to mice. Conclusions L. innocua represents a young species descending from L. monocytogenes and

  17. Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design.

    Science.gov (United States)

    Narasumani, Mohanalakshmi; Harrison, Paul M

    2015-12-18

    Intrinsic disorder occurs when (part of) a protein remains unfolded during normal functioning. Intrinsically-disordered regions can contain segments that 'fold on binding' to another molecule. Here, we perform bioinformatical parsing of human 'folding-on-binding' (FB) proteins, into four subsets: Ordered regions, FB regions, Disordered regions that surround FB regions ('Disordered-around-FB'), and Other-Disordered regions. We examined the composition and evolutionary behaviour (across vertebrate orthologs) of these subsets. From a convergence of three separate analyses, we find that for hydrophobicity, Ordered regions segregate from the other subsets, but the Ordered and FB regions group together as highly conserved, and the Disordered-around-FB and Other-Disordered regions as less conserved (with a lesser significant difference between Ordered and FB regions). FB regions are highly-conserved with net positive charge, whereas Disordered-around-FB have net negative charge and are relatively less hydrophobic than FB regions. Indeed, these Disordered-around-FB regions are excessively hydrophilic compared to other disordered regions generally. We describe how our results point towards a possible compositionally-based steering mechanism of folding-on-binding.

  18. Amino Acid Sequence and Structural Comparison of BACE1 and BACE2 Using Evolutionary Trace Method

    Directory of Open Access Journals (Sweden)

    Hoda Mirsafian

    2014-01-01

    Full Text Available Beta-amyloid precursor protein cleavage enzyme 1 (BACE1 and beta-amyloid precursor protein cleavage enzyme 2 (BACE2, members of aspartyl protease family, are close homologues and have high similarity in their protein crystal structures. However, their enzymatic properties differ leading to disparate clinical consequences. In order to identify the residues that are responsible for such differences, we used evolutionary trace (ET method to compare the amino acid conservation patterns of BACE1 and BACE2 in several mammalian species. We found that, in BACE1 and BACE2 structures, most of the ligand binding sites are conserved which indicate their enzymatic property of aspartyl protease family members. The other conserved residues are more or less randomly localized in other parts of the structures. Four group-specific residues were identified at the ligand binding site of BACE1 and BACE2. We postulated that these residues would be essential for selectivity of BACE1 and BACE2 biological functions and could be sites of interest for the design of selective inhibitors targeting either BACE1 or BACE2.

  19. Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Jelsbak, Lars;

    2015-01-01

    is suggested to be due to the large genetic repertoire of P. aeruginosa and its ability to genetically adapt to the host environment. Here, we review the recent work that has applied whole-genome sequencing to understand P. aeruginosa population genomics, within-host microevolution and diversity, mutational...... mechanisms, genetic adaptation and transmission events. Finally, we summarize the advances in relation to medical applications and laboratory evolution experiments....

  20. Improving High-Throughput Sequencing Approaches for Reconstructing the Evolutionary Dynamics of Upper Paleolithic Human Groups

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine

    been mainly driven by the development of High-Throughput DNA Sequencing (HTS) technologies but also by the implementation of novel molecular tools tailored to the manipulation of ultra short and damaged DNA molecules. Our ability to retrieve traces of genetic material has tremendously improved, pushing...... work on admixture events between Neanderthals and anatomically modern humans and but also suggested that the latter were organized in small family units whose members avoided inbreeding....

  1. Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis.

    Science.gov (United States)

    Lappin, Fiona M; Shaw, Rebecca L; Macqueen, Daniel J

    2016-12-01

    High-throughput sequencing has revolutionised comparative and evolutionary genome biology. It has now become relatively commonplace to generate multiple genomes and/or transcriptomes to characterize the evolution of large taxonomic groups of interest. Nevertheless, such efforts may be unsuited to some research questions or remain beyond the scope of some research groups. Here we show that targeted high-throughput sequencing offers a viable alternative to study genome evolution across a vertebrate family of great scientific interest. Specifically, we exploited sequence capture and Illumina sequencing to characterize the evolution of key components from the insulin-like growth (IGF) signalling axis of salmonid fish at unprecedented phylogenetic resolution. The IGF axis represents a central governor of vertebrate growth and its core components were expanded by whole genome duplication in the salmonid ancestor ~95Ma. Using RNA baits synthesised to genes encoding the complete family of IGF binding proteins (IGFBP) and an IGF hormone (IGF2), we captured, sequenced and assembled orthologous and paralogous exons from species representing all ten salmonid genera. This approach generated 299 novel sequences, most as complete or near-complete protein-coding sequences. Phylogenetic analyses confirmed congruent evolutionary histories for all nineteen recognized salmonid IGFBP family members and identified novel salmonid-specific IGF2 paralogues. Moreover, we reconstructed the evolution of duplicated IGF axis paralogues across a replete salmonid phylogeny, revealing complex historic selection regimes - both ancestral to salmonids and lineage-restricted - that frequently involved asymmetric paralogue divergence under positive and/or relaxed purifying selection. Our findings add to an emerging literature highlighting diverse applications for targeted sequencing in comparative-evolutionary genomics. We also set out a viable approach to obtain large sets of nuclear genes for any

  2. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  3. Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization.

    Science.gov (United States)

    Okuno, Miki; Kajitani, Rei; Ryusui, Rie; Morimoto, Hiroya; Kodama, Yukiko; Itoh, Takehiko

    2016-02-01

    The lager beer yeast Saccharomyces pastorianus is considered an allopolyploid hybrid species between S. cerevisiae and S. eubayanus. Many S. pastorianus strains have been isolated and classified into two groups according to geographical origin, but this classification remains controversial. Hybridization analyses and partial PCR-based sequence data have indicated a separate origin of these two groups, whereas a recent intertranslocation analysis suggested a single origin. To clarify the evolutionary history of this species, we analysed 10 S. pastorianus strains and the S. eubayanus type strain as a likely parent by Illumina next-generation sequencing. In addition to assembling the genomes of five of the strains, we obtained information on interchromosomal translocation, ploidy, and single-nucleotide variants (SNVs). Collectively, these results indicated that the two groups of strains share S. cerevisiae haploid chromosomes. We therefore conclude that both groups of S. pastorianus strains share at least one interspecific hybridization event and originated from a common parental species and that differences in ploidy and SNVs between the groups can be explained by chromosomal deletion or loss of heterozygosity.

  4. Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

    Science.gov (United States)

    Senoussi, Rachid; Simon, Vincent; Moury, Benoît

    2012-01-01

    Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts. PMID:22532800

  5. A micromorphological study of pedogenic processes in an evolutionary soil sequence formed in late quaternary rhyolitic tephra deposits, North Island, New Zealand.

    NARCIS (Netherlands)

    Bakker, L.; Lowe, D.J.; Jongmans, A.G.

    1996-01-01

    The influence of time as a soil forming factor was studied on an evolutionary sequence of five soils (1850 radiocarbo years BP-ca. 120,000 BP) developed in rhyolitic tephra deposits in New Zealand. New micromorphological observations were combined with existing macromorphological, chemical, textural

  6. Novel evolutionary lineages in Labeobarbus (Cypriniformes; Cyprinidae) based on phylogenetic analyses of mtDNA sequences.

    Science.gov (United States)

    Beshera, Kebede A; Harris, Phillip M; Mayden, Richard L

    2016-03-22

    Phylogenetic relationships within Labeobarbus, the large-sized hexaploid cyprinids, were examined using cytochrome b gene sequences from a broad range of geographic localities and multiple taxa. Maximum likelihood and Bayesian methods revealed novel lineages from previously unsampled drainages in central (Congo River), eastern (Genale River) and southeastern (Revue and Mussapa Grande rivers) Africa. Relationships of some species of Varicorhinus in Africa (excluding 'V.' maroccanus) render Labeobarbus as paraphyletic. 'Varicorhinus' beso, 'V.' jubae, 'V.' mariae, 'V.' nelspruitensis, and 'V.' steindachneri are transferred to Labeobarbus. Bayesian estimation of time to most recent common ancestor suggested that Labeobarbus originated in the Late Miocene while lineage diversification began during the Late Miocene-Early Pliocene and continued to the late Pleistocene. The relationships presented herein provide phylogenetic resolution within Labeobarbus and advances our knowledge of genetic diversity within the lineage as well as provides some interesting insight into the hydrographic and geologic history of Africa.

  7. Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia.

    Directory of Open Access Journals (Sweden)

    Sebastien Breurec

    Full Text Available The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.

  8. Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2

    Energy Technology Data Exchange (ETDEWEB)

    Dash, Paban Kumar, E-mail: pabandash@rediffmail.com; Sharma, Shashi; Soni, Manisha; Agarwal, Ankita; Parida, Manmohan; Rao, P.V.Lakshmana

    2013-07-05

    Highlights: •Complete genome of Indian DENV-2 was deciphered for the first time in this study. •The recent Indian DENV-2 revealed presence of many unique amino acid residues. •Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India. •Circulation of a unique clade of DENV-2 in South Asia was identified. -- Abstract: Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a

  9. Evolutionary models for metal-poor low-mass stars lower main sequence of globular clusters and halo field stars

    CERN Document Server

    Baraffe, I; Allard, F; Hauschildt, P H; Baraffe, Isabelle; Chabrier, Gilles; Allard, France; Hauschildt, Peter

    1997-01-01

    We have performed evolutionary calculations of very-low-mass stars from 0.08 to 0.8 $\\msol$ for different metallicites from [M/H]= -2.0 to -1.0 and we have tabulated the mechanical, thermal and photometric characteristics of these models. The calculations include the most recent interior physics and improved non-grey atmosphere models. The models reproduce the entire main sequences of the globular clusters observed with the Hubble Space Telescope over the afore-mentioned range of metallicity. Comparisons are made in the WFPC2 Flight system including the F555, F606 and F814 filters, and in the standard Johnson-Cousins system. We examine the effects of different physical parameters, mixing-length, $\\alpha$-enriched elements, helium fraction, as well as the accuracy of the photometric transformations of the HST data into standard systems. We derive mass-effective temperature and mass-magnitude relationships and we compare the results with the ones obtained with different grey-like approximations. These latter ar...

  10. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants.

    Science.gov (United States)

    Wóycicki, Rafał; Witkowicz, Justyna; Gawroński, Piotr; Dąbrowska, Joanna; Lomsadze, Alexandre; Pawełkowicz, Magdalena; Siedlecka, Ewa; Yagi, Kohei; Pląder, Wojciech; Seroczyńska, Anna; Śmiech, Mieczysław; Gutman, Wojciech; Niemirowicz-Szczytt, Katarzyna; Bartoszewski, Grzegorz; Tagashira, Norikazu; Hoshi, Yoshikazu; Borodovsky, Mark; Karpiński, Stanisław; Malepszy, Stefan; Przybecki, Zbigniew

    2011-01-01

    Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar--Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in

  11. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2011-07-01

    Full Text Available Abstract Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a genome segments unshared between B. microti and B. pinnipedialis, b gene deletion/fusion events and c positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups.

  12. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

    Science.gov (United States)

    2011-01-01

    Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups. PMID:21745361

  13. A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems.

    Science.gov (United States)

    Meng, Fanfeng; Dong, Xuan; Hu, Tao; Chang, Shuang; Fan, Jianhua; Zhao, Peng; Cui, Zhizhong

    2016-12-19

    As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully. An average of about 20,000 valid reads were obtained from two variable regions of gp85 gene and LTR-U3 region from each sample in different infectious ecosystems. The top 10 dominant variants among ALV-J from chicken plasmas, DF1 cells and liver tumor were completely different from each other. Also there was a difference of shannon entropy and global selection pressure values (ω) in different infectious ecosystems. In the plasmas of two chickens, a large portion of quasispecies contained a 3-peptides "LSD" repeat insertion that was only less than 0.01% in DF1 cell culture supernatants. In parallel studies, the LTR-U3 region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells. Our data taken together suggest that the molecular epidemiology based on isolated ALV-J in cell culture may not represent the true evolution of virus in chicken flocks in the field. The biological significance of the "LSD" insert and mutations in LTR-U3 needs to be further studied.

  14. The genome sequence of the North-European cucumber (Cucumis sativus L. unravels evolutionary adaptation mechanisms in plants.

    Directory of Open Access Journals (Sweden)

    Rafał Wóycicki

    Full Text Available Cucumber (Cucumis sativus L., a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10 and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar--Chinese Long (line 9930, Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth

  15. Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus

    Directory of Open Access Journals (Sweden)

    Brenner Sydney

    2008-03-01

    Full Text Available Abstract Background The mammalian neurohypophysial hormones, vasopressin and oxytocin are involved in osmoregulation and uterine smooth muscle contraction respectively. All jawed vertebrates contain at least one homolog each of vasopressin and oxytocin whereas jawless vertebrates contain a single neurohypophysial hormone called vasotocin. The vasopressin homolog in non-mammalian vertebrates is vasotocin; and the oxytocin homolog is mesotocin in non-eutherian tetrapods, mesotocin and [Phe2]mesotocin in lungfishes, and isotocin in ray-finned fishes. The genes encoding vasopressin and oxytocin genes are closely linked in the human and rodent genomes in a tail-to-tail orientation. In contrast, their pufferfish homologs (vasotocin and isotocin are located on the same strand of DNA with isotocin gene located upstream of vasotocin gene separated by five genes, suggesting that this locus has experienced rearrangements in either mammalian or ray-finned fish lineage, or in both lineages. The coelacanths occupy a unique phylogenetic position close to the divergence of the mammalian and ray-finned fish lineages. Results We have sequenced a coelacanth (Latimeria menadoensis BAC clone encompassing the neurohypophysial hormone genes and investigated the evolutionary history of the vertebrate neurohypophysial hormone gene locus within a comparative genomics framework. The coelacanth contains vasotocin and mesotocin genes like non-mammalian tetrapods. The coelacanth genes are present on the same strand of DNA with no intervening genes, with the vasotocin gene located upstream of the mesotocin gene. Nucleotide sequences of the second exons of the two genes are under purifying selection implying a regulatory function. We have also analyzed the neurohypophysial hormone gene locus in the genomes of opossum, chicken and Xenopus tropicalis. The opossum contains two tandem copies of vasopressin and mesotocin genes. The vasotocin and mesotocin genes in chicken and

  16. Molecular cloning, sequencing and tissue expression of vasotocin and isotocin precursor genes from Ostariophysian catfishes: Phylogeny and evolutionary considerations in teleosts

    Directory of Open Access Journals (Sweden)

    Putul eBanerjee

    2015-05-01

    Full Text Available Basic and neutral neurohypophyseal (NH nonapeptides have evolved from vasotocin (VT by a gene duplication at the base of the gnathostome lineage. In teleosts, VT and IT are the basic and neutral peptides, respectively. In the present study, VT and IT precursor genes of Heteropneustes fossilis and Clarias batrachus (Siluriformes, Ostariophysi were cloned and sequenced. The channel catfish Icatalurus punctatus NH precursor sequences were obtained from EST database. The catfish NH sequences were used along with the available Acanthopterygii and other vertebrate NH precursor sequences to draw phylogenetic inference on the evolutionary history of the teleost NH peptides. Synteny analysis of the NH gene loci in various teleost species was done to complement the phylogenetic analysis. In H. fossilis, the NH transcripts were also sequenced from the ovary. The cloned genes and the deduced precursor proteins showed conserved characteristics of the NH nonapeptide precursors. The genes are expressed in brain and ovary (follicular envelope of H. fossilis with higher transcript abundance in the brain. The addition of the catfish sequences in the phylogenetic analysis revealed that the VT and IT precursors of the species-rich superorders of teleosts have a distinct phylogenetic history with the Acanthopterygii VT and IT precursors sharing a less evolutionary distance and the Ostariophysi VT and IT having a greater evolutionary distance. The genomic location of VT and IT precursors, and synteny analysis of the NH loci lend support to the phylogenetic inference and suggest a footprint of fish- specific whole genome duplication (3R and subsequent diploidization in the NH loci. The VT and IT precursor genes are most likely lineage-specific paralogs resulting from differential losses of the 3R NH paralogs in the two superorders. The independent yet consistent retention of VT and IT in the two superorders might be directed by a stringent ligand-receptor selectivity.

  17. The evolutionary rates of HCV estimated with subtype 1a and 1b sequences over the ORF length and in different genomic regions.

    Directory of Open Access Journals (Sweden)

    Manqiong Yuan

    Full Text Available BACKGROUND: Considerable progress has been made in the HCV evolutionary analysis, since the software BEAST was released. However, prior information, especially the prior evolutionary rate, which plays a critical role in BEAST analysis, is always difficult to ascertain due to various uncertainties. Providing a proper prior HCV evolutionary rate is thus of great importance. METHODS/RESULTS: 176 full-length sequences of HCV subtype 1a and 144 of 1b were assembled by taking into consideration the balance of the sampling dates and the even dispersion in phylogenetic trees. According to the HCV genomic organization and biological functions, each dataset was partitioned into nine genomic regions and two routinely amplified regions. A uniform prior rate was applied to the BEAST analysis for each region and also the entire ORF. All the obtained posterior rates for 1a are of a magnitude of 10(-3 substitutions/site/year and in a bell-shaped distribution. Significantly lower rates were estimated for 1b and some of the rate distribution curves resulted in a one-sided truncation, particularly under the exponential model. This indicates that some of the rates for subtype 1b are less accurate, so they were adjusted by including more sequences to improve the temporal structure. CONCLUSION: Among the various HCV subtypes and genomic regions, the evolutionary patterns are dissimilar. Therefore, an applied estimation of the HCV epidemic history requires the proper selection of the rate priors, which should match the actual dataset so that they can fit for the subtype, the genomic region and even the length. By referencing the findings here, future evolutionary analysis of the HCV subtype 1a and 1b datasets may become more accurate and hence prove useful for tracing their patterns.

  18. Phylogeny and evolutionary genetics of Frankia strains based on 16S rRNA and nifD-K gene sequences.

    Science.gov (United States)

    Mishra, Arun Kumar; Singh, Pawan Kumar; Singh, Prashant; Singh, Anumeha; Singh, Satya Shila; Srivastava, Amrita; Srivastava, Alok Kumar; Sarma, Hridip Kumar

    2015-08-01

    16S rRNA and nifD-nifK sequences were used to study the molecular phylogeny and evolutionary genetics of Frankia strains isolated from Hippöphae salicifolia D. Don growing at different altitudes (ecologically classified as riverside and hillside isolates) of the Eastern Himalayan region of North Sikkim, India. Genetic information for the small subunit rRNA (16S rRNA) revealed that the riverside Frankia isolates markedly differed from the hillside isolates suggesting that the riverside isolates are genetically compact. Further, for enhanced resolutions, the partial sequence of nifD (3' end), nifK (5' end) and nifD-K IGS region have been investigated. The sequences obtained, failed to separate riverside isolates and hillside isolates, thus suggesting a possible role of genetic transfer events either from hillside to riverside or vice versa. The evolutionary genetic analyses using evogenomic extrapolations of gene sequence data obtained from 16S rRNA and nifD-K provided differing equations with the pace of evolution being more appropriately, intermediate. Values of recombination frequency (R), nucleotide diversity per site (Pi), and DNA divergence estimates supported the existence of an intermixed zone where spatial isolations occurred in sync with the temporal estimates. J. Basic Microbiol. 2015, 54, 1-9.

  19. Data on the evolutionary history of the V(DJ recombination-activating protein 1 – RAG1 coupled with sequence and variant analyses

    Directory of Open Access Journals (Sweden)

    Abhishek Kumar

    2016-09-01

    Full Text Available RAG1 protein is one of the key component of RAG complex regulating the V(DJ recombination. There are only few studies for RAG1 concerning evolutionary history, detailed sequence and mutational hotspots. Herein, we present out datasets used for the recent comprehensive study of RAG1 based on sequence, phylogenetic and genetic variant analyses (Kumar et al., 2015 [1]. Protein sequence alignment helped in characterizing the conserved domains and regions of RAG1. It also aided in unraveling ancestral RAG1 in the sea urchin. Human genetic variant analyses revealed 751 mutational hotspots, located both in the coding and the non-coding regions. For further analysis and discussion, see (Kumar et al., 2015 [1].

  20. The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis.

    Science.gov (United States)

    Komiyama, Tomoyoshi; Ikeo, Kazuho; Gojobori, Takashi

    2004-05-26

    Chickens with exceptionally long crow are often favored all over the world, and connoisseur breeders have bred certain types of chicken exclusively for this trait. In Japan, three chicken varieties have been specifically bred to develop an exceptionally long crow of over 15 s. Although these three long-crowing chickens, Naganakidori, are honored as heritage varieties of Japan, the domestication process and genealogical origin of long-crowing chickens remain unclear. The purpose of this study is to clarify these issues using nucleotide sequences of the mitochondrial DNA D-loop region. Blood samples from a total of nine long-crowing chickens and 74 chickens from 11 Japanese native varieties were collected. DNA sequence data of two Junglefowl species were also collected from the International DNA database (DDBJ /EMBL/GenBank) for use as the outgroup. A phylogenetic tree was then constructed revealing that all three Naganakidori varieties were monophyletic and originated from a fighting cock, a Shamo, for cockfighting. These results suggest that these three long-crowing chickens share a common origin in spite of their conspicuously different characters, and that human cultures favoring long-crowing chickens might have been preceded by a tradition of cockfighting. Moreover, these long-crowing varieties first separated from the fighting cocks of Okinawa, which is geographically closer to Southern China and Indochina than Mainland Japan (Honshu/Kyushu). This implies that Japanese long-crowing chickens were first brought to Mainland Japan as fighting cocks from the surrounding regions of Southern China or Indochina and through Okinawa.

  1. NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

    DEFF Research Database (Denmark)

    Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

    2010-01-01

    NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which......-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC = 0.50, Qtotal = 82.1%, sensitivity = 75.6%, PPV = 68.8% and AUC = 0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17 – 0.......47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively....

  2. Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae).

    Science.gov (United States)

    Botero-Castro, Fidel; Tilak, Marie-ka; Justy, Fabienne; Catzeflis, François; Delsuc, Frédéric; Douzery, Emmanuel J P

    2013-12-01

    Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of

  3. The rotation period distributions of 4--10 Myr T Tauri stars in Orion OB1: New constraints on pre-main-sequence angular momentum evolution

    CERN Document Server

    Karim, Md Tanveer; Briceno, Cesar; Vivas, A Katherina; Raetz, Stefanie; Mateu, Cecilia; Downes, Juan Jose; Calvet, Nuria; Hernandez, Jesus; Neuhauser, Ralph; Mugrauer, Markus; Takahashi, Hidenori; Tachihara, Kengo; Chini, Rolf; Cruz-Dias, Gustavo A; Aarnio, Alicia; James, David J; Hackstein, Moritz

    2016-01-01

    Most existing studies of the angular momentum evolution of young stellar populations have focused on the youngest (1-3 Myr) T Tauri stars. In contrast, the angular momentum distributions of older T Tauri stars (4-10 Myr) have been less studied, even though they hold key insight to understanding stellar angular momentum evolution at a time when protoplanetary disks have largely dissipated and when models therefore predict changes in the rotational evolution that can in principle be tested. We present a study of photometric variability among 1,974 confirmed T Tauri members of various sub-regions of the Orion OB1 association, and with ages spanning 4-10 Myr, using optical time-series from three different surveys. For 564 of the stars (~32% of the weak-lined T Tauri stars and ~13% of the classical T Tauri stars in our sample) we detect statistically significant periodic variations which we attribute to the stellar rotation periods, making this one of the largest samples of T Tauri star rotation periods yet publis...

  4. Evidence for Variable, Correlated X-ray and Optical/IR Extinction toward the Nearby, Pre-main Sequence Binary TWA 30

    CERN Document Server

    Principe, David A; Kastner, Joel H; Stelzer, Beate; Alcala, Juan

    2016-01-01

    We present contemporaneous XMM-Newton X-ray and ground-based optical/near-IR spectroscopic observations of the nearby ($D \\approx 42$ pc), low-mass (mid-M) binary system TWA 30A and 30B. The components of this wide (separation $\\sim$3400 AU) binary are notable for their nearly edge-on disk viewing geometries, high levels of variability, and evidence for collimated stellar outflows. We obtained XMM-Newton X-ray observations of TWA 30A and 30B in 2011 June and July, accompanied (respectively) by IRTF SpeX (near-IR) and VLT XSHOOTER (visible/near-IR) spectroscopy obtained within $\\sim$20 hours of the X-ray observations. TWA 30A was detected in both XMM-Newton observations at relatively faint intrinsic X-ray luminosities ($L_{X}$$\\sim$$8\\times10^{27}$ $erg$ $s^{-1}$) compared to stars of similar mass and age . The intrinsic (0.15-2.0 keV) X-ray luminosities measured in 2011 had decreased by a factor 20-100 relative to a 1990 (ROSAT) X-ray detection. TWA 30B was not detected, and we infer an upper limit of ($L_{X}...

  5. The Rotation Period Distributions of 4-10 Myr T Tauri Stars in Orion OB1: New Constraints on Pre-main-sequence Angular Momentum Evolution

    Science.gov (United States)

    Karim, Md Tanveer; Stassun, Keivan G.; Briceño, César; Vivas, A. Katherina; Raetz, Stefanie; Mateu, Cecilia; José Downes, Juan; Calvet, Nuria; Hernández, Jesús; Neuhäuser, Ralph; Mugrauer, Markus; Takahashi, Hidenori; Tachihara, Kengo; Chini, Rolf; Cruz-Dias, Gustavo A.; Aarnio, Alicia; James, David J.; Hackstein, Moritz

    2016-12-01

    Most existing studies of the angular momentum evolution of young stellar populations have focused on the youngest (≲1-3 Myr) T Tauri stars. In contrast, the angular momentum distributions of older T Tauri stars (˜4-10 Myr) have been less studied, even though they hold key insights to understanding stellar angular momentum evolution at a time when protoplanetary disks have largely dissipated and when models therefore predict changes in the rotational evolution that can in principle be tested. We present a study of photometric variability among 1974 confirmed T Tauri members of various subregions of the Orion OB1 association, and with ages spanning 4-10 Myr, using optical time series from three different surveys. For 564 of the stars (˜32% of the weak-lined T Tauri stars and ˜13% of the classical T Tauri stars in our sample) we detect statistically significant periodic variations, which we attribute to the stellar rotation periods, making this one of the largest samples of T Tauri star rotation periods yet published. We observe a clear change in the overall rotation period distributions over the age range 4-10 Myr, with the progressively older subpopulations exhibiting systematically faster rotation. This result is consistent with angular momentum evolution model predictions of an important qualitative change in the stellar rotation periods starting at ˜5 Myr, an age range for which very few observational constraints were previously available.

  6. TIME-SERIES PHOTOMETRY OF STARS IN AND AROUND THE LAGOON NEBULA. I. ROTATION PERIODS OF 290 LOW-MASS PRE-MAIN-SEQUENCE STARS IN NGC 6530

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Calen B. [Department of Astronomy, Ohio State University, 140 W. 18th Ave., Columbus, OH 43210 (United States); Stassun, Keivan G., E-mail: henderson@astronomy.ohio-state.edu [Department of Physics and Astronomy, Vanderbilt University, VU Station B 1807, Nashville, TN 37235 (United States)

    2012-03-01

    We have conducted a long-term, wide-field, high-cadence photometric monitoring survey of {approx}50,000 stars in the Lagoon Nebula H II region. This first paper presents rotation periods for 290 low-mass stars in NGC 6530, the young cluster illuminating the nebula, and for which we assemble a catalog of infrared and spectroscopic disk indicators, estimated masses and ages, and X-ray luminosities. The distribution of rotation periods we measure is broadly uniform for 0.5 days < P < 10 days; the short-period cutoff corresponds to breakup. We observe no obvious bimodality in the period distribution, but we do find that stars with disk signatures rotate more slowly on average. The stars' X-ray luminosities are roughly flat with rotation period, at the saturation level (log L{sub X} /L{sub bol} Almost-Equal-To -3.3). However, we find a significant positive correlation between L{sub X} /L{sub bol} and corotation radius, suggesting that the observed X-ray luminosities are regulated by centrifugal stripping of the stellar coronae. The period-mass relationship in NGC 6530 is broadly similar to that of the Orion Nebula Cluster (ONC), but the slope of the relationship among the slowest rotators differs from that in the ONC and other young clusters. We show that the slope of the period-mass relationship for the slowest rotators can be used as a proxy for the age of a young cluster, and we argue that NGC 6530 may be slightly younger than the ONC, making it a particularly important touchstone for models of angular momentum evolution in young, low-mass stars.

  7. Optical spectroscopy of X-ray sources in the Taurus molecular cloud: discovery of ten new pre-main sequence stars

    CERN Document Server

    Scelsi, L; Affer, L; Argiroffi, C; Pillitteri, I; Maggio, A; Micela, G

    2008-01-01

    We have analyzed optical spectra of 25 X-ray sources identified as potential new members of the Taurus molecular cloud (TMC), in order to confirm their membership in this SFR. Fifty-seven candidates were previously selected among the X-ray sources in the XEST survey, having a 2MASS counterpart compatible with a PMS star based on color-magnitude and color-color diagrams. We obtained high-resolution optical spectra for 7 of these candidates with the SARG spectrograph at the TNG telescope, which were used to search for Li absorption and to measure the Ha line and the radial and rotational velocities; 18 low-resolution optical spectra obtained with DOLORES for other candidate members were used for spectral classification, for Ha measurements, and to assess membership together with IR color-color and color-magnitude diagrams and additional information from the X-ray data. We found that 3 sources show Li absorption, with equivalent widths of ~500 mA, broad spectral line profiles, indicating v sin i ~20-40 km/s, rad...

  8. Time-Series Photometry of Stars in and around the Lagoon Nebula. I. Rotation Periods of 290 Low-Mass Pre-Main-Sequence Stars in NGC 6530

    CERN Document Server

    Henderson, Calen B

    2011-01-01

    We have conducted a long-term, wide-field, high-cadence photometric monitoring survey of ~50,000 stars in the Lagoon Nebula \\ion{H}{2} region. This first paper presents rotation periods for 290 low-mass stars in NGC 6530, the young cluster illuminating the nebula, and for which we assemble a catalog of infrared and spectroscopic disk indicators, estimated masses and ages, and X-ray luminosities. The distribution of rotation periods we measure is broadly uniform for 0.5 < P < 10 d; the short-period cutoff corresponds to breakup. We observe no obvious bimodality in the period distribution, but we do find that stars with disk signatures rotate more slowly on average. The stars' X-ray luminosities are roughly flat with rotation period, at the saturation level ($\\log L_X / L_{\\rm bol} \\approx -3.3$). However, we find a significant positive correlation between $L_X / L_{\\rm bol}$ and co-rotation radius, suggesting that the observed X-ray luminosities are regulated by centrifugal stripping of the stellar coron...

  9. LUMINOSITY DISCREPANCY IN THE EQUAL-MASS, PRE-MAIN-SEQUENCE ECLIPSING BINARY PAR 1802: NON-COEVALITY OR TIDAL HEATING?

    Energy Technology Data Exchange (ETDEWEB)

    Gomez Maqueo Chew, Yilen; Stassun, Keivan G.; Hebb, Leslie [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Prsa, Andrej [Department of Astronomy and Astrophysics, Villanova University, Villanova, PA 19085 (United States); Stempels, Eric [Department of Astronomy and Space Physics, Uppsala University, SE-752 67 Uppsala (Sweden); Barnes, Rory [Department of Astronomy, University of Washington, Seattle, WA 98195 (United States); Heller, Rene [Leibniz-Institut fuer Astrophysik Potsdam (AIP), An der Sternwarte 16, 14482 Potsdam (Germany); Mathieu, Robert D., E-mail: yilen.gomez@vanderbilt.edu [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2012-01-20

    Parenago 1802, a member of the {approx}1 Myr Orion Nebula Cluster, is a double-lined, detached eclipsing binary in a 4.674 day orbit, with equal-mass components (M{sub 2}/M{sub 1} = 0.985 {+-} 0.029). Here we present extensive VI{sub C} JHK{sub S} light curves (LCs) spanning {approx}15 yr, as well as a Keck/High Resolution Echelle Spectrometer (HIRES) optical spectrum. The LCs evince a third light source that is variable with a period of 0.73 days, and is also manifested in the high-resolution spectrum, strongly indicating the presence of a third star in the system, probably a rapidly rotating Classical T Tauri star. We incorporate this third light into our radial velocity and LC modeling of the eclipsing pair, measuring accurate masses (M{sub 1} = 0.391 {+-} 0.032 and M{sub 2} = 0.385 {+-} 0.032 M{sub Sun }), radii (R{sub 1} = 1.73 {+-} 0.02 and R{sub 2} = 1.62 {+-} 0.02 R{sub Sun }), and temperature ratio (T{sub eff,1}/T{sub eff,2} = 1.0924 {+-} 0.0017). Thus, the radii of the eclipsing stars differ by 6.9% {+-} 0.8%, the temperatures differ by 9.2% {+-} 0.2%, and consequently the luminosities differ by 62% {+-} 3%, despite having masses equal to within 3%. This could be indicative of an age difference of {approx}3 Multiplication-Sign 10{sup 5} yr between the two eclipsing stars, perhaps a vestige of the binary formation history. We find that the eclipsing pair is in an orbit that has not yet fully circularized, e = 0.0166 {+-} 0.003. In addition, we measure the rotation rate of the eclipsing stars to be 4.629 {+-} 0.006 days; they rotate slightly faster than their 4.674 day orbit. The non-zero eccentricity and super-synchronous rotation suggest that the eclipsing pair should be tidally interacting, so we calculate the tidal history of the system according to different tidal evolution theories. We find that tidal heating effects can explain the observed luminosity difference of the eclipsing pair, providing an alternative to the previously suggested age difference.

  10. Variability of Disk Emission in Pre-Main Sequence and Related Stars. II. Variability in the Gas and Dust Emission of the Herbig Fe Star SAO 206462

    CERN Document Server

    Sitko, Michael L; Kimes, Robin L; Beerman, Lori C; Martus, Cameron; Lynch, David K; Russell, Ray W; Grady, Carol A; Schneider, Glenn; Lisse, Carey M; Nuth, Joseph A; Cure, Michel; Henden, Arne A; Kraus, Stefan; Motta, Veronica; Tamura, Motohide; Hornbeck, Jeremy; Williger, Gerard M; Fugazza, Dino

    2011-01-01

    We present thirteen epochs of near-infrared (0.8-5 micron) spectroscopic observations of the pre-transitional, "gapped" disk system in SAO 206462 (=HD 135344B). In all, six gas emission lines (including Br gamma, Pa beta, and the 0.8446 micron line of O I) along with continuum measurements made near the standard J, H, K, and L photometric bands were measured. A mass accretion rate of approximately 2 x 10^-8 solar masses per year was derived from the Br gamma and Pa beta lines. However, the fluxes of these lines varied by a factor of over two during the course of a few months. The continuum also varied, but by only ~30%, and even decreased at a time when the gas emission was increasing. The H I line at 1.083 microns was also found to vary in a manner inconsistent with that of either the hydrogen lines or the dust. Both the gas and dust variabilities indicate significant changes in the region of the inner gas and the inner dust belt that may be common to many young disk systems. If planets are responsible for d...

  11. Variability of Disk Emission in Pre-Main Sequence and Related Stars. III. Exploring Structural Changes in the Pre-transitional Disk in HD 169142

    CERN Document Server

    Wagner, Kevin R; Grady, Carol A; Whitney, Barbara A; Swearingen, Jeremy R; Champney, Elizabeth H; Johnson, Alexa N; Werren, Chelsea; Russell, Ray W; Schneider, Glenn H; Momose, Munetake; Muto, Takayuki; Inoue, Akio K; Lauroesch, James T; Brown, Alexander; Fukagawa, Misato; Currie, Thayne M; Hornbeck, Jeremy; Wisniewski, John P; Woodgate, Bruce E

    2014-01-01

    We present near-IR and far-UV observations of the pre-transitional (gapped) disk in HD 169142 using NASA's Infrared Telescope Facility and Hubble Space Telescope. The combination of our data along with existing data sets into the broadband spectral energy distribution reveals variability of up to 45% between ~1.5-10 {\\mu}m over a maximum timescale of 10 years. All observations known to us separate into two distinct states corresponding to a high near-IR state in the pre-2000 epoch and a low state in the post-2000 epoch, indicating activity within the <1 AU region of the disk. Through analysis of the Pa {\\beta} and Br {\\gamma} lines in our data we derive a mass accretion rate in May 2013 of (1.5 - 2.7) x 10^-9 Msun/yr. We present a theoretical modeling analysis of the disk in HD 169142 using Monte-Carlo radiative transfer simulation software to explore the conditions and perhaps signs of planetary formation in our collection of 24 years of observations. We find that shifting the outer edge (r = 0.3 AU) of t...

  12. Evidence for variable, correlated X-ray and optical/IR extinction towards the nearby, pre-main-sequence binary TWA 30

    Science.gov (United States)

    Principe, David A.; Sacco, G.; Kastner, J. H.; Stelzer, B.; Alcalá, J. M.

    2016-06-01

    We present contemporaneous XMM-Newton X-ray and ground-based optical/near-IR spectroscopic observations of the nearby (D ≈ 42 pc), low-mass (mid-M) binary system TWA 30A and 30B. The components of this wide (separation ˜3400 au) binary are notable for their nearly edge-on disc viewing geometries, high levels of variability, and evidence for collimated stellar outflows. We obtained XMM-Newton X-ray observations of TWA 30A and 30B in 2011 June and July, accompanied (respectively) by Infrared Telescope Facility SpeX (near-IR) and VLT XSHOOTER (visible/near-IR) spectroscopy obtained within ˜20 h of the X-ray observations. TWA 30A was detected in both XMM-Newton observations at relatively faint intrinsic X-ray luminosities (LX ˜ 8 × 1027 erg s-1) compared to stars of similar mass and age. The intrinsic (0.15-2.0 keV) X-ray luminosities measured in 2011 had decreased by a factor 20-100 relative to a 1990 (ROSAT) X-ray detection. TWA 30B was not detected, and we infer an upper limit on its X-ray Luminosity of LX ≲ 3.0 × 1027 erg s-1. We measured a decrease in visual extinction towards TWA 30A (from AV ≈ 14.9 to AV ≈ 4.7) between the two 2011 observing epochs, and we find evidence for a corresponding significant decrease in X-ray absorbing column (NH). The apparent correlated change in AV and NH is suggestive of variable obscuration of the stellar photosphere by disc material composed of both gas and dust. However, in both observations, the inferred NH to AV ratio is lower than that typical of the interstellar medium, suggesting that the disc is either depleted of gas or is deficient in metals in the gas phase.

  13. Variability of Disk Emission in Pre-main Sequence and Related Stars. V. Changes in the Innermost Disk Structure of the Herbig AE Star HD 31648 = MWC 480

    Science.gov (United States)

    Fernandes, Rachel; Long, Zachary; Sitko, Michael L.; Grady, C. A.; Kusakabe, Nobuhiko

    2017-01-01

    We present five epochs of near IR observations of the protoplanetary disk around HD 31648 (MWC 480). A mass accretion rate of approximately 1.1×10-7 Msun/year was derived from Brγ and Paβ lines. The spectral energy distribution (SED) reveals a variability of about 30% between 1.5 and 10 microns. We present the theoretical modeling analysis of the disk in HD 31648 using Monte-Carlo Radiation Transfer Code (MRTC). We find that varying the height of the inner rim successfully produces a shift in the NIR flux.

  14. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)

    DEFF Research Database (Denmark)

    Jacobsen, Magnus W.; Hansen, Michael Møller; Orlando, Ludovic;

    2012-01-01

    the evolutionary history of the endangered Danish North Sea houting (NSH) and other closely related Danish and Baltic European lake whitefish (ELW). Two well-supported clades were found within both ELW and NSH, probably reflecting historical introgression via Baltic migrants. Although ELW and NSH...... colonized Denmark following the last glacial maximum, Bayesian Serial SimCoal analysis showed consistency with a scenario of long-term stability, resulting from a rapid initial sixfold population expansion. The findings illustrate the utility of mitogenome data for resolving recent intraspecific divergence...

  15. An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5' UTRs and its implications for eukaryotic gene translation regulation.

    Science.gov (United States)

    Pánek, Josef; Kolár, Michal; Vohradský, Jirí; Shivaya Valásek, Leos

    2013-09-01

    There are several key mechanisms regulating eukaryotic gene expression at the level of protein synthesis. Interestingly, the least explored mechanisms of translational control are those that involve the translating ribosome per se, mediated for example via predicted interactions between the ribosomal RNAs (rRNAs) and mRNAs. Here, we took advantage of robustly growing large-scale data sets of mRNA sequences for numerous organisms, solved ribosomal structures and computational power to computationally explore the mRNA-rRNA complementarity that is statistically significant across the species. Our predictions reveal highly specific sequence complementarity of 18S rRNA sequences with mRNA 5' untranslated regions (UTRs) forming a well-defined 3D pattern on the rRNA sequence of the 40S subunit. Broader evolutionary conservation of this pattern may imply that 5' UTRs of eukaryotic mRNAs, which have already emerged from the mRNA-binding channel, may contact several complementary spots on 18S rRNA situated near the exit of the mRNA binding channel and on the middle-to-lower body of the solvent-exposed 40S ribosome including its left foot. We discuss physiological significance of this structurally conserved pattern and, in the context of previously published experimental results, propose that it modulates scanning of the 40S subunit through 5' UTRs of mRNAs.

  16. 5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

    Science.gov (United States)

    Van den Eynde, H.; De Baere, R.; Shah, H. N.; Gharbia, S. E.; Fox, G. E.; Michalik, J.; Van de Peer, Y.; De Wachter, R.

    1989-01-01

    The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

  17. Evolutionary history of Triticum petropavlovskyi Udacz. et Migusch. inferred from the sequences of the 3-phosphoglycerate kinase gene.

    Directory of Open Access Journals (Sweden)

    Qian Chen

    Full Text Available Single- and low-copy genes are less likely to be subject to concerted evolution. Thus, they are appropriate tools to study the origin and evolution of polyploidy plant taxa. The plastid 3-phosphoglycerate kinase gene (Pgk-1 sequences from 44 accessions of Triticum and Aegilops, representing diploid, tetraploid, and hexaploid wheats, were used to estimate the origin of Triticum petropavlovskyi. Our phylogenetic analysis was carried out on exon+intron, exon and intron sequences, using maximum likelihood, Bayesian inference and haplotype networking. We found the D genome sequences of Pgk-1 genes from T. petropavlovskyi are similar to the D genome orthologs in T. aestivum, while their relationship with Ae. tauschii is more distant. The A genome sequences of T. petropavlovskyi group with those of T. polonicum, but its Pgk-1 B genome sequences to some extent diverge from those of other species of Triticum. Our data do not support for the origin of T. petropavlovskyi either as an independent allopolyploidization event between Ae. tauschii and T. polonicum, or as a monomendelian mutation in T. aestivum. We suggest that T. petropavlovskyi originated via spontaneous introgression from T. polonicum into T. aestivum. The dating of divergence among T. polonicum, T. petropavlovskyi, T. carthlicum, T. turgidum, and T. compactum indicates an age of 0.78 million years [corrected].

  18. Multi-Objective Analysis Applied to Mixed-Model Assembly Line Sequencing Problem through Elite Induced Evolutionary Method

    Science.gov (United States)

    Shimizu, Yoshiaki; Sakaguchi, Tatsuhiko; Pralomkarn, Theerayoth

    To meet higher customer satisfaction and shorter production lead time, assembly lines are shifting to mixed-model assembly lines. Accordingly, sequencing is becoming an increasingly important operation scheduling that directly affects on efficiency of the entire process. In this study, such sequencing problem at the mixed-model assembly line has been formulated as a bi-objective integer programming problem so that decision making through trade-off analysis can bring about significant production improvements. Then we have developed a multi-objective analysis method by hybridizing conventional and recent meta-heuristic methods. After showing its generic idea, the car mixed-model assembly line sequencing problem is concerned as a case study. Certain measures are also introduced to quantitatively evaluate the performances of the method through comparison.

  19. Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization.

    Science.gov (United States)

    Sergeeva, Ekaterina M; Salina, Elena A; Adonina, Irina G; Chalhoub, Boulos

    2010-07-01

    Mobile elements constitute a considerable part of the eukaryotic genome. This work is focused on the distribution and evolution of DNA-transposons in the genomes of diploid and allopolyploid Triticeae species and their role in the formation of functionally important chromosomal subtelomeric regions. The Caspar family is among the most abundant of CACTA DNA-transposons in Triticeae. To study the evolution of Caspar-like elements in Triticeae genomes, we analyzed their sequences and distribution in chromosomes by in situ hybridization. In total, 46 Caspar-like elements from the wheat and barley Caspar, Clifford, and Donald families were analyzed after being extracted from databases using the transposase consensus sequence. Sequence alignment and subsequent phylogenetic analyses revealed that the transposase DNA sequences formed three major distinct groups: (1) Clifford, (2) Caspar_Triticinae, and (3) Caspar_Hordeinae. Additionally, in situ hybridization demonstrated that Caspar_Triticinae transposons are predominantly compartmentalized in the subtelomeric chromosomal regions of wheat and its progenitors. Analysis of data suggested that compartmentalization in the subtelomeric chromosomal region was a characteristic feature of all the main groups of Caspar-like elements. Furthermore, a dot plot analysis of the terminal repeats demonstrated that the divergence of these repeats strictly correlated with the divergence of Caspar coding sequences. A clear distinction in the Caspar DNA sequences among the species Triticum/Aegilops (Caspar_Triticinae), Hordeum (Caspar_Hordeinae), and different distributions in individual hexaploid wheat genomes (A/B and D) suggest an independent proliferation of these elements in wheat (or its progenitors) and barley genomes. Thus, Caspar-like transposons can significantly contribute to the formation and differentiation of subtelomeric regions in Triticeae species.

  20. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

    Directory of Open Access Journals (Sweden)

    Leila do Nascimento Vieira

    Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

  1. The Complete Chloroplast Genome Sequence of Podocarpus lambertii: Genome Structure, Evolutionary Aspects, Gene Content and SSR Detection

    Science.gov (United States)

    Vieira, Leila do Nascimento; Faoro, Helisson; Rogalski, Marcelo; Fraga, Hugo Pacheco de Freitas; Cardoso, Rodrigo Luis Alves; de Souza, Emanuel Maltempi; de Oliveira Pedrosa, Fábio; Nodari, Rubens Onofre; Guerra, Miguel Pedro

    2014-01-01

    Background Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. Methodology/Principal Findings The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. Conclusion The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus. PMID

  2. Different evolutionary pathway of B*570101 and B*5801 (B17 group) alleles based in intron sequences.

    Science.gov (United States)

    Martinez-Laso, Jorge; Moscoso, Juan; Zamora, Jorge; Martin-Villa, Manuel; Lowy, Ernesto; Vargas-Alarcon, Gilberto; Serrano-Vela, Juan Ignacio; Gomez-Casado, Eduardo; Arnaiz-Villena, Antonio

    2004-03-01

    Two theories about MHC allele generation have been put forward: (1) point mutation diversification and/or (2) gene conversion events. A model supporting the existence of both of these mechanisms is shown in this paper; the possible evolution of the HLA-B*570101 and HLA-B*5801 alleles (which belong to the HLA-B17 serology group) is studied. The hypothesis favoured is that gene conversion events have originated these alleles, because intron sequences are also analysed. Evolution by point mutation should only be accepted if flanking introns have also been sequenced.

  3. Putative recombination events and evolutionary history of five economically important viruses of fruit trees based on coat protein-encoding gene sequence analysis.

    Science.gov (United States)

    Boulila, Moncef

    2010-06-01

    To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31beta algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary.

  4. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

    Science.gov (United States)

    Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

  5. Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of Iridoviridae

    Directory of Open Access Journals (Sweden)

    Wang Xiujie

    2009-05-01

    Full Text Available Abstract Background Soft-shelled turtle iridovirus (STIV is the causative agent of severe systemic diseases in cultured soft-shelled turtles (Trionyx sinensis. To our knowledge, the only molecular information available on STIV mainly concerns the highly conserved STIV major capsid protein. The complete sequence of the STIV genome is not yet available. Therefore, determining the genome sequence of STIV and providing a detailed bioinformatic analysis of its genome content and evolution status will facilitate further understanding of the taxonomic elements of STIV and the molecular mechanisms of reptile iridovirus pathogenesis. Results We determined the complete nucleotide sequence of the STIV genome using 454 Life Science sequencing technology. The STIV genome is 105 890 bp in length with a base composition of 55.1% G+C. Computer assisted analysis revealed that the STIV genome contains 105 potential open reading frames (ORFs, which encode polypeptides ranging from 40 to 1,294 amino acids and 20 microRNA candidates. Among the putative proteins, 20 share homology with the ancestral proteins of the nuclear and cytoplasmic large DNA viruses (NCLDVs. Comparative genomic analysis showed that STIV has the highest degree of sequence conservation and a colinear arrangement of genes with frog virus 3 (FV3, followed by Tiger frog virus (TFV, Ambystoma tigrinum virus (ATV, Singapore grouper iridovirus (SGIV, Grouper iridovirus (GIV and other iridovirus isolates. Phylogenetic analysis based on conserved core genes and complete genome sequence of STIV with other virus genomes was performed. Moreover, analysis of the gene gain-and-loss events in the family Iridoviridae suggested that the genes encoded by iridoviruses have evolved for favoring adaptation to different natural host species. Conclusion This study has provided the complete genome sequence of STIV. Phylogenetic analysis suggested that STIV and FV3 are strains of the same viral species belonging to the

  6. Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily

    Directory of Open Access Journals (Sweden)

    Wei-Jun Chen

    2015-01-01

    Full Text Available CCCH zinc finger proteins, which are characterized by the presence of three cysteine residues and one histidine residue, play important roles in RNA processing in plants. Subfamily IX CCCH proteins were recently shown to function in stress tolerances. In this study, we analyzed CCCH IX genes in Zea mays, Oryza sativa, and Sorghum bicolor. These genes, which are almost intronless, were divided into four groups based on phylogenetic analysis. Microsynteny analysis revealed microsynteny in regions of some gene pairs, indicating that segmental duplication has played an important role in the expansion of this gene family. In addition, we calculated the dates of duplication by Ks analysis, finding that all microsynteny blocks were formed after the monocot-eudicot divergence. We found that deletions, multiplications, and inversions were shown to have occurred over the course of evolution. Moreover, the Ka/Ks ratios indicated that the genes in these three grass species are under strong purifying selection. Finally, we investigated the evolutionary patterns of some gene pairs conferring tolerance to abiotic stress, laying the foundation for future functional studies of these transcription factors.

  7. Microfossils from the Neoarchean Campbell Group, Griqualand West Sequence of the Transvaal Supergroup, and their paleoenvironmental and evolutionary implications

    Science.gov (United States)

    Altermann, W.; Schopf, J. W.

    1995-01-01

    The oldest filament- and colonial coccoid-containing microbial fossil assemblage now known is described here from drill core samples of stromatolitic cherty limestones of the Neoarchean, approximately 2600-Ma-old Campbell Group (Ghaap Plateau Dolomite, Lime Acres Member) obtained at Lime Acres, northern Cape Province, South Africa. The assemblage is biologically diverse, including entophysalidacean (Eoentophysalis sp.), probable chroococcacean (unnamed colonial coccoids), and oscillatoriacean cyanobacteria (Eomycetopsis cf. filiformis, and Siphonophycus transvaalensis), as well as filamentous fossil bacteria (Archaeotrichion sp.); filamentous possible microfossils (unnamed hematitic filaments) also occur. The Campbell Group microorganisms contributed to the formation of stratiform and domical to columnar stromatolitic reefs in shallow subtidal to intertidal environments of the Transvaal intracratonic sea. Although only moderately to poorly preserved, they provide new evidence regarding the paleoenvironmental setting of the Campbell Group sediments, extend the known time-range of entophysalidacean cyanobacteria by more than 400 million years, substantiate the antiquity and role in stromatolite formation of Archean oscillatoriacean cyanobacteria, and document the exceedingly slow (hypobradytelic) evolutionary rate characteristic of this early evolving prokaryotic lineage.

  8. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: Utility and potential for the discovery of novel evolutionary patterns

    KAUST Repository

    Malik, Assaf

    2011-08-12

    The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ~12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat. 2011 Malik et al.

  9. Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns.

    Directory of Open Access Journals (Sweden)

    Assaf Malik

    Full Text Available The blind subterranean mole rat (Spalax ehrenbergi superspecies is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ∼12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat.

  10. Evolutionary dynamics of Anolis sex chromosomes revealed by sequencing of flow sorting-derived microchromosome-specific DNA.

    Science.gov (United States)

    Kichigin, Ilya G; Giovannotti, Massimo; Makunin, Alex I; Ng, Bee L; Kabilov, Marsel R; Tupikin, Alexey E; Barucchi, Vincenzo Caputo; Splendiani, Andrea; Ruggeri, Paolo; Rens, Willem; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A; Graphodatsky, Alexander S; Trifonov, Vladimir A

    2016-10-01

    Squamate reptiles show a striking diversity in modes of sex determination, including both genetic (XY or ZW) and temperature-dependent sex determination systems. The genomes of only a handful of species have been sequenced, analyzed and assembled including the genome of Anolis carolinensis. Despite a high genome coverage, only macrochromosomes of A. carolinensis were assembled whereas the content of most microchromosomes remained unclear. Most of the Anolis species have homomorphic XY sex chromosome system. However, some species have large heteromorphic XY chromosomes (e.g., A. sagrei) and even multiple sex chromosomes systems (e.g. A. pogus), that were shown to be derived from fusions of the ancestral XY with microautosomes. We applied next generation sequencing of flow sorting-derived chromosome-specific DNA pools to characterize the content and composition of microchromosomes in A. carolinensis and A. sagrei. Comparative analysis of sequenced chromosome-specific DNA pools revealed that the A. sagrei XY sex chromosomes contain regions homologous to several microautosomes of A. carolinensis. We suggest that the sex chromosomes of A. sagrei are derived by fusions of the ancestral sex chromosome with three microautosomes and subsequent loss of some genetic content on the Y chromosome.

  11. Sequence analysis of 96 genomic regions identifies distinct evolutionary lineages within CC156, the largest Streptococcus pneumoniae clonal complex in the MLST database.

    Directory of Open Access Journals (Sweden)

    Monica Moschioni

    Full Text Available Multi-Locus Sequence Typing (MLST of Streptococcus pneumoniae is based on the sequence of seven housekeeping gene fragments. The analysis of MLST allelic profiles by eBURST allows the grouping of genetically related strains into Clonal Complexes (CCs including those genotypes with a common descent from a predicted ancestor. However, the increasing use of MLST to characterize S. pneumoniae strains has led to the identification of a large number of new Sequence Types (STs causing the merger of formerly distinct lineages into larger CCs. An example of this is the CC156, displaying a high level of complexity and including strains with allelic profiles differing in all seven of the MLST loci, capsular type and the presence of the Pilus Islet-1 (PI-1. Detailed analysis of the CC156 indicates that the identification of new STs, such as ST4945, induced the merging of formerly distinct clonal complexes. In order to discriminate the strain diversity within CC156, a recently developed typing schema, 96-MLST, was used to analyse 66 strains representative of 41 different STs. Analysis of allelic profiles by hierarchical clustering and a minimum spanning tree identified ten genetically distinct evolutionary lineages. Similar results were obtained by phylogenetic analysis on the concatenated sequences with different methods. The identified lineages are homogenous in capsular type and PI-1 presence. ST4945 strains were unequivocally assigned to one of the lineages. In conclusion, the identification of new STs through an exhaustive analysis of pneumococcal strains from various laboratories has highlighted that potentially unrelated subgroups can be grouped into a single CC by eBURST. The analysis of additional loci, such as those included in the 96-MLST schema, will be necessary to accurately discriminate the clonal evolution of the pneumococcal population.

  12. Pulsating low-mass white dwarfs in the frame of new evolutionary sequences. IV. The secular rate of period change

    Science.gov (United States)

    Calcaferro, Leila M.; Córsico, Alejandro H.; Althaus, Leandro G.

    2017-04-01

    Context. An increasing number of low-mass (M⋆/M⊙ ≲ 0.45) and extremely low-mass (ELM, M⋆/M⊙ ≲ 0.18-0.20) white-dwarf stars are being discovered in the field of the Milky Way. Some of these stars exhibit long-period g-mode pulsations, and are called ELMV variable stars. Also, some low-mass pre-white dwarf stars show short-period p-mode (and likely radial-mode) photometric variations, and are designated as pre-ELMV variable stars. The existence of these new classes of pulsating white dwarfs and pre-white dwarfs opens the prospect of exploring the binary formation channels of these low-mass white dwarfs through asteroseismology. Aims: We aim to present a theoretical assessment of the expected temporal rates of change of periods (\\dot{Π}) for such stars, based on fully evolutionary low-mass He-core white dwarf and pre-white dwarf models. Methods: Our analysis is based on a large set of adiabatic periods of radial and nonradial pulsation modes computed on a suite of low-mass He-core white dwarf and pre-white dwarf models with masses ranging from 0.1554 to 0.4352 M⊙, which were derived by computing the non-conservative evolution of a binary system consisting of an initially 1 M⊙ ZAMS star and a 1.4 M⊙ neutron star companion. Results: We computed the secular rates of period change of radial (ℓ = 0) and nonradial (ℓ = 1,2) g and p modes for stellar models representative of ELMV and pre-ELMV stars, as well as for stellar objects that are evolving just before the occurrence of CNO flashes at the early cooling branches. We find that the theoretically expected magnitude of \\dot{Π} of g modes for pre-ELMVs is by far larger than for ELMVs. In turn, \\dot{Π} of g modes for models evolving before the occurrence of CNO flashes are larger than the maximum values of the rates of period change predicted for pre-ELMV stars. Regarding p and radial modes, we find that the larger absolute values of \\dot{Π} correspond to pre-ELMV models. Conclusions: We

  13. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Godoy, Daniel; Randle, Gaynor; Simpson, Andrew J; Aanensen, David M; Pitt, Tyrone L; Kinoshita, Reimi; Spratt, Brian G

    2003-05-01

    A collection of 147 isolates of Burkholderia pseudomallei, B. mallei, and B. thailandensis was characterized by multilocus sequence typing (MLST). The 128 isolates of B. pseudomallei, the causative agent of melioidosis, were obtained from diverse geographic locations, from humans and animals with disease, and from the environment and were resolved into 71 sequence types. The utility of the MLST scheme for epidemiological investigations was established by analyzing isolates from captive marine mammals and birds and from humans in Hong Kong with melioidosis. MLST gave a level of resolution similar to that given by pulsed-field gel electrophoresis and identified the same three clones causing disease in animals, each of which was also associated with disease in humans. The average divergence between the alleles of B. thailandensis and B. pseudomallei was 3.2%, and there was no sharing of alleles between these species. Trees constructed from differences in the allelic profiles of the isolates and from the concatenated sequences of the seven loci showed that the B. pseudomallei isolates formed a cluster of closely related lineages that were fully resolved from the cluster of B. thailandensis isolates, confirming their separate species status. However, isolates of B. mallei, the causative agent of glanders, recovered from three continents over a 30-year period had identical allelic profiles, and the B. mallei isolates clustered within the B. pseudomallei group of isolates. Alleles at six of the seven loci in B. mallei were also present within B. pseudomallei isolates, and B. mallei is a clone of B. pseudomallei that, on population genetics grounds, should not be given separate species status.

  14. A hybrid multi-objective evolutionary algorithm approach for handling sequence- and machine-dependent set-up times in unrelated parallel machine scheduling problem

    Indian Academy of Sciences (India)

    V K MANUPATI; G RAJYALAKSHMI; FELIX T S CHAN; J J THAKKAR

    2017-03-01

    This paper addresses a fuzzy mixed-integer non-linear programming (FMINLP) model by considering machine-dependent and job-sequence-dependent set-up times that minimize the total completion time,the number of tardy jobs, the total flow time and the machine load variation in the context of unrelated parallel machine scheduling (UPMS) problem. The above-mentioned multi-objectives were considered based on nonzero ready times, machine- and sequence-dependent set-up times and secondary resource constraints for jobs.The proposed approach considers unrelated parallel machines with inherent uncertainty in processing times and due dates. Since the problem is shown to be NP-hard in nature, it is a challenging task to find the optimal/nearoptimal solutions for conflicting objectives simultaneously in a reasonable time. Therefore, we introduced a new multi-objective-based evolutionary artificial immune non-dominated sorting genetic algorithm (AI-NSGA-II) to resolve the above-mentioned complex problem. The performance of the proposed multi-objective AI-NSGA-II algorithm has been compared to that of multi-objective particle swarm optimization (MOPSO) and conventionalnon-dominated sorting genetic algorithm (CNSGA-II), and it is found that the proposed multi-objective-based hybrid meta-heuristic produces high-quality solutions. Finally, the results obtained from benchmark instances and randomly generated instances as test problems evince the robust performance of the proposed multiobjective algorithm.

  15. Optimization of binary sequences based on evolutionary algorithm%基于进化计算的二元序列优化算法研究

    Institute of Scientific and Technical Information of China (English)

    李鹤; 李琦; 高军萍; 雷明然

    2014-01-01

    具有良好非周期自相关特性二元序列在通信同步、雷达等领域具有广泛的应用。通过对遗传算法、粒子群算法与量子粒子群算法三种进化算法进行对比分析,设计了具有良好非周期自相关特性的二元序列的搜索算法。研究结果表明,粒子群算法的搜索能力优于遗传算法,而量子粒子群算法具有参数少,易于控制的优点,取得了较好的优化结果。%Binary sequences with good aperiodic autocorrelation features are widely used in the field of radar, communication synchronization. Genetic algorithm, particle swarm optimization and quantum particle swarm optimization algorithm are compared and analyzed in this paper. The new search algorithm of binary sequences with good aperiodic autocorrelation properties are designed based on three evolutionary algorithms. Research results show that the search ability of particle swarm algorithm is better than genetic algorithm. Quantum particle swarm optimization algorithm has less parameters, easy to control, and the better good optimization results were obtained.

  16. Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America

    Science.gov (United States)

    Haley, Bradd J.; Kim, Seon Woo; Pettengill, James; Luo, Yan; Karns, Jeffrey S.; Van Kessel, Jo Ann S.

    2016-01-01

    Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals. PMID:27695032

  17. A "living fossil" sequence: primary structure of the coelacanth (Latimeria chalumnae) hemoglobin--evolutionary and functional aspects.

    Science.gov (United States)

    Gorr, T; Kleinschmidt, T; Sgouros, J G; Kasang, L

    1991-08-01

    The coelacanth (Latimeria chalumnae, Actinistia) has a single hemoglobin component. The primary structures of the alpha- and beta-chains are presented. They could be separated by reversed-phase HPLC. Peptides obtained by tryptic digestion of the native and oxidized chains were isolated by reversed-phase HPLC and sequenced in liquid and gas-phase sequenators. The alignment was achieved by employing the N-terminal sequences of the native chains and those of a beta-chain cyanogen bromide peptide as well as fragments obtained by acid hydrolysis. The Latimeria alpha-chains consist of 142 amino-acid residues, due to a fish-specific insertion between positions 46 and 47, whereas the beta-chains are of normal length (146 residues). Latimeria alpha- and beta-chains share 72 (51.1%) and 70 (47.9%) identical residues with human hemoglobin, respectively. Numerous heme contacts and positions involved in subunit interface contacts are replaced. The most interesting of them were studied by molecular modeling. The loss of an alpha 1/beta 2-contact by the exchanges alpha 92(FG4)Arg----Leu and beta 43(CD2)Glu----Lys might be responsible for the easy dissociation of the tetrameric hemoglobin molecule. A comparison of the residues replaced in contact positions with fishes and amphibians revealed the highest number of matches between Latimeria and tadpoles. The same result was obtained by the evaluation of other regions relevant for structure and function of the molecule, like exon-intron boundary regions, phosphate binding sites and salt bridges responsible for the Bohr effect.

  18. Multilocus Sequence Typing Reveals Relevant Genetic Variation and Different Evolutionary Dynamics among Strains of Xanthomonas arboricola pv. juglandis

    Directory of Open Access Journals (Sweden)

    Marco Scortichini

    2010-11-01

    Full Text Available Forty-five Xanthomonas arboricola pv. juglandis (Xaj strains originating from Juglans regia cultivation in different countries were molecularly typed by means of MultiLocus Sequence Typing (MLST, using acnB, gapA, gyrB and rpoD gene fragments. A total of 2.5 kilobases was used to infer the phylogenetic relationship among the strains and possible recombination events. Haplotype diversity, linkage disequilibrium analysis, selection tests, gene flow estimates and codon adaptation index were also assessed. The dendrograms built by maximum likelihood with concatenated nucleotide and amino acid sequences revealed two major and two minor phylotypes. The same haplotype was found in strains originating from different continents, and different haplotypes were found in strains isolated in the same year from the same location. A recombination breakpoint was detected within the rpoD gene fragment. At the pathovar level, the Xaj populations studied here are clonal and under neutral selection. However, four Xaj strains isolated from walnut fruits with apical necrosis are under diversifying selection, suggesting a possible new adaptation. Gene flow estimates do not support the hypothesis of geographic isolation of the strains, even though the genetic diversity between the strains increases as the geographic distance between them increases. A triplet deletion, causing the absence of valine, was found in the rpoD fragment of all 45 Xaj strains when compared with X. axonopodis pv. citri strain 306. The codon adaptation index was high in all four genes studied, indicating a relevant metabolic activity.

  19. K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.

    Science.gov (United States)

    Sievers, Aaron; Bosiek, Katharina; Bisch, Marc; Dreessen, Chris; Riedel, Jascha; Froß, Patrick; Hausmann, Michael; Hildenbrand, Georg

    2017-04-19

    In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of

  20. Evolutionary relationships within the protostome phylum Sipuncula: a molecular analysis of ribosomal genes and histone H3 sequence data.

    Science.gov (United States)

    Maxmen, Amy B; King, Burnett F; Cutler, Edward B; Giribet, Gonzalo

    2003-06-01

    The phylogenetic relationships of the members of the phylum Sipuncula are investigated by means of DNA sequence data from three nuclear markers, two ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), and one protein-coding gene, histone H3. Phylogenetic analysis via direct optimization of DNA sequence data using parsimony as optimality criterion is executed for 12 combinations of parameter sets accounting for different indel costs and transversion/transition cost ratios in a sensitivity analysis framework. Alternative outgroup analyses are also performed to test whether they affected rooting of the sipunculan topology. Nodal support is measured by parsimony jackknifing and Bremer support values. Results from the different partitions are highly congruent, and the combined analysis for the parameter set that minimizes overall incongruence supports monophyly of Sipuncula, but nonmonophyly of several higher taxa recognized for the phylum. Mostly responsible for this is the split of the family Sipunculidae in three main lineages, with the genus Sipunculus being the sister group to the remaining sipunculans, the genus Phascolopsis nesting within the Golfingiiformes, and the genus Siphonosoma being associated to the Phascolosomatidea. Other interesting results are the position of Phascolion within Golfingiidae and the position of Antillesoma within Aspidosiphonidae. These results are not affected by the loci selected or by the outgroup chosen. The position of Apionsoma is discussed, although more data would be needed to better ascertain its phylogenetic affinities. Monophyly of the genera with multiple representatives (Themiste, Aspidosiphon, and Phascolosoma) is well supported, but not the monophyly of the genera Nephasoma or Golfingia. Interesting phylogeographic questions arise from analysis of multiple representatives of a few species.

  1. Antennal RNA-sequencing analysis reveals evolutionary aspects of chemosensory proteins in the carpenter ant, Camponotus japonicus.

    Science.gov (United States)

    Hojo, Masaru K; Ishii, Kenichi; Sakura, Midori; Yamaguchi, Katsushi; Shigenobu, Shuji; Ozaki, Mamiko

    2015-08-27

    Chemical communication is essential for the coordination of complex organisation in ant societies. Recent comparative genomic approaches have revealed that chemosensory genes are diversified in ant lineages, and suggest that this diversification is crucial for social organisation. However, how such diversified genes shape the peripheral chemosensory systems remains unknown. In this study, we annotated and analysed the gene expression profiles of chemosensory proteins (CSPs), which transport lipophilic compounds toward chemosensory receptors in the carpenter ant, Camponotus japonicus. Transcriptome analysis revealed 12 CSP genes and phylogenetic analysis showed that 3 of these are lineage-specifically expanded in the clade of ants. RNA sequencing and real-time quantitative polymerase chain reaction revealed that, among the ant specific CSP genes, two of them (CjapCSP12 and CjapCSP13) were specifically expressed in the chemosensory organs and differentially expressed amongst ant castes. Furthermore, CjapCSP12 and CjapCSP13 had a ratio of divergence at non-synonymous and synonymous sites (dN/dS) greater than 1, and they were co-expressed with CjapCSP1, which is known to bind cuticular hydrocarbons. Our results suggested that CjapCSP12 and CjapCSP13 were functionally differentiated for ant-specific chemosensory events, and that CjapCSP1, CjapCSP12, and CjapCSP13 work cooperatively in the antennal chemosensilla of worker ants.

  2. Reconstruction of the Evolutionary History of Saccharomyces cerevisiae x S. kudriavzevii Hybrids Based on Multilocus Sequence Analysis

    Science.gov (United States)

    Peris, David; Lopes, Christian A.; Arias, Armando; Barrio, Eladio

    2012-01-01

    In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages. PMID:23049811

  3. Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis.

    Science.gov (United States)

    Peris, David; Lopes, Christian A; Arias, Armando; Barrio, Eladio

    2012-01-01

    In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages.

  4. The Activity of the Neighbours of AGN and Starburst Galaxies: Towards an evolutionary sequence of AGN activity

    CERN Document Server

    Koulouridis, E; Chavushyan, V; Dultzin, D; Krongold, Y; Georgantopoulos, I; Goudis, C

    2009-01-01

    We present a follow-up study of a series of papers concerning the role of close interactions as a possible triggering mechanism of the activity of AGN and starburst (SB) galaxies. We have already studied the close (<100 kpc) and the large scale (<1 Mpc) environment of Sy1, Sy2 and Bright IRAS galaxies and their respective control samples (Koulouridis et al.). The results led us to the conclusion that a close encounter appears capable of activating a sequence where a normal galaxy becomes first a starburst, then a Sy2 and finally a Sy1 galaxy. However since both galaxies of an interacting pair should be affected, we present here optical spectroscopy and X-ray imaging of the neighbouring galaxies around our Seyfert and BIRG galaxy samples. We find that more than 70% of all neighbouring galaxies exhibit thermal or/and nuclear activity (namely enhanced star formation, starbursting and/or AGN) and furthermore we discovered various trends regarding the type and strength of the neighbour's activity with respec...

  5. H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Zwick Matthias

    2008-03-01

    Full Text Available Abstract Background A multiple sequence alignment (MSA generated for a protein can be used to characterise residues by means of a statistical analysis of single columns. In addition to the examination of individual positions, the investigation of co-variation of amino acid frequencies offers insights into function and evolution of the protein and residues. Results We introduce conn(k, a novel parameter for the characterisation of individual residues. For each residue k, conn(k is the number of most extreme signals of co-evolution. These signals were deduced from a normalised mutual information (MI value U(k, l computed for all pairs of residues k, l. We demonstrate that conn(k is a more robust indicator than an individual MI-value for the prediction of residues most plausibly important for the evolution of a protein. This proposition was inferred by means of statistical methods. It was further confirmed by the analysis of several proteins. A server, which computes conn(k-values is available at http://www-bioinf.uni-regensburg.de. Conclusion The algorithms H2r, which analyses MSAs and computes conn(k-values, characterises a specific class of residues. In contrast to strictly conserved ones, these residues possess some flexibility in the composition of side chains. However, their allocation is sensibly balanced with several other positions, as indicated by conn(k.

  6. Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis.

    Directory of Open Access Journals (Sweden)

    David Peris

    Full Text Available In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages.

  7. Evolutionary relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA gene sequences.

    Science.gov (United States)

    Dowton, M; Austin, A D; Antolin, M F

    1998-05-01

    Phylogenetic relationships among the Braconidae were examined using homologous 16S rDNA gene sequence data. Analyses recovered the few well-supported relationships evident in this family from morphological analyses, viz the monophyly of the microgastroid complex of subfamilies, the monophyly of the cyclostome complex of subfamilies (= braconoids), a sister-group relationship between the Alysiinae and Opiinae, and a close relationship between the Helconinae and Blacinae. With respect to the braconoid complex of subfamilies, a sister-group relationship was recovered between Aphidiinae and Mesostoinae, and a clade composed of Gnamptodontinae + Histeromerinae + Rhyssalinae + Aphidiinae + Mesostoinae was also recovered. The Doryctinae and Rogadinae sensu lato (s.l.) were generally not resolved as monophyletic. With respect to the helconoid complex of subfamilies, a sister-group relationship was recovered between Sigalphinae and Agathidinae, whereas Neoneurinae fell out among other helconoid subfamilies. Other relationships among the helconoid subfamilies were unclear from these analyses. With respect to the microgastroid complex of subfamilies, our data conform to morphological estimates, recovering ((Microgastrinae + Miracinae) + Cardiochilinae) + Cheloninae. The topology of our trees suggests that the cyclostome subfamilies are a natural derived group, inferring that endoparasitism (not ectoparasitism) is the ancestral state for the Braconidae, unless all of the ectoparasitic ancestors of the helconoid + microgastroid subfamilies are now extinct.

  8. SNP detection from de novo transcriptome sequencing in the bivalve Macoma balthica: marker development for evolutionary studies.

    Directory of Open Access Journals (Sweden)

    Eric Pante

    Full Text Available Hybrid zones are noteworthy systems for the study of environmental adaptation to fast-changing environments, as they constitute reservoirs of polymorphism and are key to the maintenance of biodiversity. They can move in relation to climate fluctuations, as temperature can affect both selection and migration, or remain trapped by environmental and physical barriers. There is therefore a very strong incentive to study the dynamics of hybrid zones subjected to climate variations. The infaunal bivalve Macoma balthica emerges as a noteworthy model species, as divergent lineages hybridize, and its native NE Atlantic range is currently contracting to the North. To investigate the dynamics and functioning of hybrid zones in M. balthica, we developed new molecular markers by sequencing the collective transcriptome of 30 individuals. Ten individuals were pooled for each of the three populations sampled at the margins of two hybrid zones. A single 454 run generated 277 Mb from which 17K SNPs were detected. SNP density averaged 1 polymorphic site every 14 to 19 bases, for mitochondrial and nuclear loci, respectively. An [Formula: see text] scan detected high genetic divergence among several hundred SNPs, some of them involved in energetic metabolism, cellular respiration and physiological stress. The high population differentiation, recorded for nuclear-encoded ATP synthase and NADH dehydrogenase as well as most mitochondrial loci, suggests cytonuclear genetic incompatibilities. Results from this study will help pave the way to a high-resolution study of hybrid zone dynamics in M. balthica, and the relative importance of endogenous and exogenous barriers to gene flow in this system.

  9. NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

    Science.gov (United States)

    Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

    2010-01-01

    β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC  = 0.50, Qtotal = 82.1%, sensitivity  = 75.6%, PPV  = 68.8% and AUC  = 0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17 – 0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. Conclusion The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences. PMID:21152409

  10. NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.

    Directory of Open Access Journals (Sweden)

    Bent Petersen

    Full Text Available UNLABELLED: β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. CONCLUSION: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.

  11. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-01-01

    Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  12. Pulsating low-mass white dwarfs in the frame of new evolutionary sequences: III. The pre-ELM white dwarf instability strip

    CERN Document Server

    Córsico, A H; Serenelli, A M; Kepler, S O; Jeffery, C S; Corti, M A

    2016-01-01

    Two low-mass pre-white dwarfs, which could be precursors of ELM white dwarfs, have been observed to show multiperiodic photometric variations. They could constitute a new class of pulsating low-mass pre-white dwarf stars. We present a detailed nonadiabatic pulsation study of such stars, employing full evolutionary sequences of low-mass He-core pre-white dwarf models. We have considered models in which element diffusion is accounted for and also models in which it is neglected. We confirm and explore in detail a new instability strip in the domain of low gravities and low effective temperatures of the $T_{\\rm eff}-\\log g$ diagram, where low-mass pre-white dwarfs are currently found. The destabilized modes are radial and nonradial $p$ and $g$ modes excited by the $\\kappa-\\gamma$ mechanism acting mainly at the zone of the second partial ionization of He, with non-negligible contributions from the region of the first partial ionization of He and the partial ionization of H. The computations with element diffusion...

  13. Molecular phylogeography and evolutionary history of Picea likiangensis in the Qinghai-Tibetan Plateau inferred from mitochondrial and chloroplast DNA sequence variation

    Institute of Scientific and Technical Information of China (English)

    Jia-Bin ZOU; Xiao-Li PENG; Long LI; Jian-Quan LIU; Georg MIEHE; Lars OPGENOORTH

    2012-01-01

    The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis,a dominant species of the conifer forests in the eastern declivity of the Qinghai-Tibetan Plateau.We collected 422 individuals from 42 natural populations of three major varieties classified under this species.In conifers,mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow.To this end,we examined the sequence variation of two mtDNA fragments (nad5 intron 1 and nadl intron b/c) and three cpDNA fragments (trnL-trnF,trnS-trnG and nadhK/C).We found that cpDNA probably introgressed from P.purpurea into remote populations of P.likiangensis through long-distance dispersal.Multiple refugia seem to have been maintained for P.likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions.Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations.However,genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions,which may result from the long-distance dispersal of the cpDNA,as well as its fast lineage sorting during intraspecific divergences.Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers,which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa.Together,the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion,long-distance dispersal,and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.

  14. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary...

  15. Tracing the evolutionary lineage of pattern recognition receptor homologues in vertebrates: An insight into reptilian immunity via de novo sequencing of the wall lizard splenic transcriptome.

    Science.gov (United States)

    Priyam, Manisha; Tripathy, Mamta; Rai, Umesh; Ghorai, Soma Mondal

    2016-04-01

    Reptiles remain a deprived class in the area of genomic and molecular resources for the vertebrate classes. The transition of squamates from aquatic to terrestrial mode of life caused profound changes in their immune system to combat the altered variety of pathogens on land. The current study aims at delineating the evolution of defence mechanisms in wall lizard, Hemidactylus flaviviridis, by exploring its immunome. De novo sequencing of splenic transcriptome from wall lizard on the Illumina Hi-Seq platform generated 258,128 unique transcripts with an average GC content of 45%. Annotation of 555,557 and 6812 transcripts was carried out against NCBI (non-redundant database) and UniProt databases, respectively. The KEGG pathway annotation of transcripts classified them into 39 processes of six pathway function categories. A total of 3824 transcripts, involved in 23 immune-related pathways, were identified in the immune-relevant cluster built by harvesting the genes under KEGG pathways of immune system and immune diseases. Forty-two percent of the immune-relevant cluster was represented by pattern-recognition receptors (PRRs), of which the maximum number of transcripts was attributed to the Toll-like receptor (TLR) signalling pathway. Nine PRRs with potential full-length coding sequences were sorted for phylogenetic analysis and comparative domain analysis across the vertebrate lineage. They included DEC205/lymphocyte antigen 75 (ly75), nucleotide-binding oligomerisation domain-containing protein 1 (NOD1), NOD-like receptor family CARD domain-containing 3 (NLRC3), nucleotide-binding oligomerisation domain, leucine-rich repeat-containing X1 (NLRX1), DDX58/retinoic acid-inducible gene 1 (RIG-1), Toll-like receptor 3 (TLR3), TLR4, TLR5 and TLR7. From selection studies of these genes, we inferred positive selection for ly75, NOD1, RIG-1, TLR3 and TLR4. Apart from contributing to the scarce genomic resources available for reptiles and giving a broad scope for the immune

  16. Evolutionary Demography

    DEFF Research Database (Denmark)

    Levitis, Daniel

    2015-01-01

    of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...

  17. Circumstellar disks during various evolutionary stages

    CERN Document Server

    Oudmaijer, Rene D

    2013-01-01

    Disks are ubiquitous in stellar astronomy, and play a crucial role in the formation and evolution of stars. In this contribution we present an overview of the most recent results, with emphasis on high spatial and spectral resolution. We will start with a general discussion on direct versus indirect detection of disks, and then traverse the HR diagram starting with the pre-Main Sequence and ending with evolved stars.

  18. Evolutionary Awareness

    Directory of Open Access Journals (Sweden)

    Gregory Gorelik

    2014-10-01

    Full Text Available In this article, we advance the concept of “evolutionary awareness,” a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities—which we refer to as “intergenerational extended phenotypes”—by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  19. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  20. Evolutionary awareness.

    Science.gov (United States)

    Gorelik, Gregory; Shackelford, Todd K

    2014-08-27

    In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment.

  1. Evolutionary Expectations

    DEFF Research Database (Denmark)

    Nash, Ulrik William

    2014-01-01

    The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover......, they are correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical...... expectations emphasizes not only that causal structure changes are common in social systems but also that causal structures in social systems, and expectations about them, develop together....

  2. Evolutionary medicine.

    Science.gov (United States)

    Swynghedauw, B

    2004-04-01

    Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.

  3. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana

    OpenAIRE

    Bush, Stephen J; Kover, Paula X.; Urrutia, Araxi O.

    2015-01-01

    Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relat...

  4. Sequence and RT-PCR expression analysis of two peroxidases from Arabidopsis thaliana belonging to a novel evolutionary branch of plant perioxidases

    DEFF Research Database (Denmark)

    Kjærsgård, I.V.H.; Jespersen, H.M.; Rasmussen, Søren Kjærsgård;

    1997-01-01

    cDNA clones encoding two new Arabidopsis thaliana peroxidases, ATP la and ATP 2a, have been identified by searching the Arabidopsis database of expressed sequence tags (dbEST). They represent a novel branch of hitherto uncharacterized plant peroxidases which is only 35% identical in amino acid...... of unknown function, is likely to be widespread in plant species. The atp 1 and atp 2 types of cDNA sequences were the most redundant among the 28 different isoperoxidases identified among about 200 peroxidase encoding ESTs. Interestingly, 8 out of totally 38 EST sequences coding for ATP 1 showed three...... sequence to the well characterized group of basic plant peroxidases represented by the horseradish (Armoracia rusticana) isoperoxidases HRP C, HRP E5 and the similar Arabidopsis isoperoxidases ATP Ca, ATP Cb, and ATP Ea. However ATP 1a is 87% identical in amino acid sequence to a peroxidase encoded by an m...

  5. An internal part of the chloroplast atpA gene sequence is present in the mitochondrial genome of Triticum aestivum: molecular organisation and evolutionary aspects.

    Science.gov (United States)

    Jubier, M F; Lucas, H; Delcher, E; Hartmann, C; Quétier, F; Lejeune, B

    1990-06-01

    An internal part of the chloroplast atpA gene has been identified in the mitochondrial DNA of Triticum aestivum. It is located near the 18S-5S ribosomal genes and partially contained within a repeated sequence. Comparison of the transferred sequence with the original ct sequence reveals several nucleotide changes and shows that neither 5' nor 3' ends are present in the mt genome. No transcript of this region could be detected by Northern analysis. This sequence is present in mitochondrial genomes of other tetraploid and diploid species of Triticum, also in the vicinity of the 18S-5S ribosomal genes, suggesting a unique transfer event. The date of this event is discussed.

  6. Evolutionary thinking

    OpenAIRE

    Hunt, Tam

    2015-01-01

    Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this de...

  7. Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations

    Directory of Open Access Journals (Sweden)

    Accili Eric A

    2008-06-01

    Full Text Available Abstract Background Mutations in HERG and KCNQ1 potassium channels have been associated with Long QT syndrome and atrial fibrillation, and more recently with sudden infant death syndrome and sudden unexplained death. In other proteins, disease-associated amino acid mutations have been analyzed according to the chemical severity of the changes and the locations of the altered amino acids according to their conservation over metazoan evolution. Here, we present the first such analysis of arrhythmia-associated mutations (AAMs in the HERG and KCNQ1 potassium channels. Results Using evolutionary analyses, AAMs in HERG and KCNQ1 were preferentially found at evolutionarily conserved sites and unevenly distributed among functionally conserved domains. Non-synonymous single nucleotide polymorphisms (nsSNPs are under-represented at evolutionarily conserved sites in HERG, but distribute randomly in KCNQ1. AAMs are chemically more severe, according to Grantham's Scale, than changes observed in evolution and their severity correlates with the expected chemical severity of the involved codon. Expected chemical severity of a given amino acid also correlates with its relative contribution to arrhythmias. At evolutionarily variable sites, the chemical severity of the changes is also correlated with the expected chemical severity of the involved codon. Conclusion Unlike nsSNPs, AAMs preferentially locate to evolutionarily conserved, and functionally important, sites and regions within HERG and KCNQ1, and are chemically more severe than changes which occur in evolution. Expected chemical severity may contribute to the overrepresentation of certain residues in AAMs, as well as to evolutionary change.

  8. Identification of distant Agouti-like sequences and re-evaluation of the evolutionary history of the Agouti-related peptide (AgRP.

    Directory of Open Access Journals (Sweden)

    Åke Västermark

    Full Text Available The Agouti-like peptides including AgRP, ASIP and the teleost-specific A2 (ASIP2 and AgRP2 peptides have potent and diverse functional roles in feeding, pigmentation and background adaptation mechanisms. There are contradictory theories about the evolution of the Agouti-like peptide family as well the nomenclature. Here we performed comprehensive mining and annotation of vertebrate Agouti-like sequences. We identified A2 sequences from salmon, trout, seabass, cod, cichlid, tilapia, gilt-headed sea bream, Antarctic toothfish, rainbow smelt, common carp, channel catfish and interestingly also in lobe-finned fish. Moreover, we surprisingly found eight novel homologues from the kingdom of arthropods and three from fungi, some sharing the characteristic C-x(6-C-C motif which are present in the Agouti-like sequences, as well as approximate sequence length (130 amino acids, positioning of the motif sequence and sharing of exon-intron structures that are similar to the other Agouti-like peptides providing further support for the common origin of these sequences. Phylogenetic analysis shows that the AgRP sequences cluster basally in the tree, suggesting that these sequences split from a cluster containing both the ASIP and the A2 sequences. We also used a novel approach to determine the statistical evidence for synteny, a sinusoidal Hough transform pattern recognition technique. Our analysis shows that the teleost AgRP2 resides in a chromosomal region that has synteny with Hsa 8, but we found no convincing synteny between the regions that A2, AgRP and ASIP reside in, which would support that the Agouti-like peptides were formed by whole genome tetraplodization events. Here we suggest that the Agouti-like peptide genes were formed through classical subsequent gene duplications where the AgRP is the most distantly related to the three other members of that group, first splitting from a common ancestor to ASIP and A2, and then later the A2 split from ASIP

  9. The Extreme Ultraviolet and X-Ray Sun in Time: High-Energy Evolutionary Tracks of a Solar-Like Star

    CERN Document Server

    Tu, Lin; Güdel, Manuel; Lammer, Helmut

    2015-01-01

    Aims. We aim to describe the pre-main sequence and main-sequence evolution of X-ray and extreme-ultaviolet radiation of a solar mass star based on its rotational evolution starting with a realistic range of initial rotation rates. Methods. We derive evolutionary tracks of X-ray radiation based on a rotational evolution model for solar mass stars and the rotation-activity relation. We compare these tracks to X-ray luminosity distributions of stars in clusters with different ages. Results. We find agreement between the evolutionary tracks derived from rotation and the X-ray luminosity distributions from observations. Depending on the initial rotation rate, a star might remain at the X-ray saturation level for very different time periods, approximately from 10 Myr to 300 Myr for slow and fast rotators, respectively. Conclusions. Rotational evolution with a spread of initial conditions leads to a particularly wide distribution of possible X-ray luminosities in the age range of 20 to 500 Myrs, before rotational co...

  10. The extreme ultraviolet and X-ray Sun in Time: High-energy evolutionary tracks of a solar-like star

    Science.gov (United States)

    Tu, Lin; Johnstone, Colin P.; Güdel, Manuel; Lammer, Helmut

    2015-05-01

    Aims: We aim to describe the pre-main-sequence and main-sequence evolution of X-ray and extreme-ultaviolet radiation of a solar-mass star based on its rotational evolution starting with a realistic range of initial rotation rates. Methods: We derive evolutionary tracks of X-ray radiation based on a rotational evolution model for solar-mass stars and the rotation-activity relation. We compare these tracks to X-ray luminosity distributions of stars in clusters with different ages. Results: We find agreement between the evolutionary tracks derived from rotation and the X-ray luminosity distributions from observations. Depending on the initial rotation rate, a star might remain at the X-ray saturation level for very different time periods, from ≈10 Myr to ≈300 Myr for slow and fast rotators, respectively. Conclusions: Rotational evolution with a spread of initial conditions leads to a particularly wide distribution of possible X-ray luminosities in the age range of 20-500 Myr, before rotational convergence and therefore X-ray luminosity convergence sets in. This age range is crucial for the evolution of young planetary atmospheres and may thus lead to very different planetary evolution histories.

  11. A METHOD OF GENERATING CHAOTIC SEQUENCES BASED ON THE NEURAL NETWORK AND EVOLUTIONARY PROGRAMMING%基于神经网络和进化算法的混沌序列产生方法

    Institute of Scientific and Technical Information of China (English)

    万继宏; 刘国钦

    2001-01-01

    Based on the strong learning ability and nonlinear function approximation capacity of Multi-Layer Perceptrons (MLPs), a generating chaotic sequence model is proposed in this paper. The chaos generation neural network model and synaptic weights database have been built to generate many chaotic sequences trained by the Evolutionary Programming (EP) algorithm with various discrete chaotic time series. Experimental results show that this EP-trained MLP model can generate a chaotic series, whose attractor can be reconstructed better than that generated by the BP-trained MLP model and which generates many chaotic sequences by changing weights of this MLPs very easily.%应用具有全局最优的进化规划算法建立产生混沌序列的优化神经网络模型。该模型利用神经网络权值调整的灵活性,能够在同一网络结构中产生的多种混沌序列。计算机仿真结果表明:该模型比BP算法训练的神经网络模型能更好地重构混沌吸引子,调整网络权值即可产生多种混沌序列。

  12. Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

    Science.gov (United States)

    Mulder, Kevin P.; Cortazar-Chinarro, Maria; Harris, D. James; Crottini, Angelica; Grant, Evan H. Campbell; Fleischer, Robert C.; Savage, Anna E.

    2017-01-01

    The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

  13. Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Punita Sharma

    2015-12-01

    Full Text Available In prokaryotes, horizontal gene transfer (HGT has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito.

  14. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Sudarsana Poojari

    Full Text Available A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L. cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s associated with this emerging disease, designated as grapevine redleaf disease (GRD. High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV, and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.

  15. Nucleotide sequence of the Syrian hamster intracisternal A-particle gene: close evolutionary relationship of type A particle gene to types B and D oncovirus genes.

    Science.gov (United States)

    Ono, M; Toh, H; Miyata, T; Awaya, T

    1985-08-01

    We determined the complete nucleotide sequence of the intracisternal A-particle gene, IAP-H18, cloned from the normal Syrian hamster liver DNA. IAP-H18 was 7,951 base pairs in length with two identical long terminal repeats of 376 base pairs at both ends. On the coding strand, imperfect open reading frames corresponding to gag and pol of the retrovirus genome were observed, whereas many stop codons were present in the region corresponding to env. The putative H18 gag gene (809 amino acids) had a sequence homologous to the N-terminal half of the mouse mammary tumor virus gag gene and locally to the Rous sarcoma virus gag gene. The putative H18 pol gene (900 residues) was homologous to the Rous sarcoma virus pol gene almost throughout the entire region. Two conserved regions among the retrovirus pol genes have been reported. One presumably corresponds to the DNA polymerase and the RNase H domain, and the other corresponds to the DNA endonuclease domain of the multifunctional protein pol. By the comparison of the deduced amino acid sequences of the putative endonuclease domain of six representative oncovirus genomes, a phylogenetic tree of the oncovirus genomes was constructed, and the intracisternal A-particle (type A) genome was found to be more closely related to the mouse mammary tumor virus (type B) and squirrel monkey retrovirus (type D) genomes.

  16. Metagenomic shotgun sequencing of a Bunyavirus in wild-caught Aedes aegypti from Thailand informs the evolutionary and genomic history of the Phleboviruses.

    Science.gov (United States)

    Chandler, James Angus; Thongsripong, Panpim; Green, Amy; Kittayapong, Pattamaporn; Wilcox, Bruce A; Schroth, Gary P; Kapan, Durrell D; Bennett, Shannon N

    2014-09-01

    Arthropod-borne viruses significantly impact human health. They span multiple families, all of which include viruses not known to cause disease. Characterizing these representatives could provide insights into the origins of their disease-causing counterparts. Field-caught Aedes aegypti mosquitoes from Nakhon Nayok, Thailand, underwent metagenomic shotgun sequencing to reveal a Bunyavirus closely related to Phasi Charoen (PhaV) virus, isolated in 2009 from Ae. aegypti near Bangkok. Phylogenetic analysis of this virus suggests it is basal to the Phlebovirus genus thus making it ideally positioned phylogenetically for understanding the evolution of these clinically important viruses. Genomic analysis finds that a gene necessary for virulence in vertebrates, but not essential for viral replication in arthropods, is missing. The sequencing of this phylogenetically-notable and genomically-unique Phlebovirus from wild mosquitoes exemplifies the utility and efficacy of metagenomic shotgun sequencing for virus characterization in arthropod vectors of human diseases. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  17. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Noushin Niknafs

    2015-10-01

    Full Text Available Recent improvements in next-generation sequencing of tumor samples and the ability to identify somatic mutations at low allelic fractions have opened the way for new approaches to model the evolution of individual cancers. The power and utility of these models is increased when tumor samples from multiple sites are sequenced. Temporal ordering of the samples may provide insight into the etiology of both primary and metastatic lesions and rationalizations for tumor recurrence and therapeutic failures. Additional insights may be provided by temporal ordering of evolving subclones--cellular subpopulations with unique mutational profiles. Current methods for subclone hierarchy inference tightly couple the problem of temporal ordering with that of estimating the fraction of cancer cells harboring each mutation. We present a new framework that includes a rigorous statistical hypothesis test and a collection of tools that make it possible to decouple these problems, which we believe will enable substantial progress in the field of subclone hierarchy inference. The methods presented here can be flexibly combined with methods developed by others addressing either of these problems. We provide tools to interpret hypothesis test results, which inform phylogenetic tree construction, and we introduce the first genetic algorithm designed for this purpose. The utility of our framework is systematically demonstrated in simulations. For most tested combinations of tumor purity, sequencing coverage, and tree complexity, good power (≥ 0.8 can be achieved and Type 1 error is well controlled when at least three tumor samples are available from a patient. Using data from three published multi-region tumor sequencing studies of (murine small cell lung cancer, acute myeloid leukemia, and chronic lymphocytic leukemia, in which the authors reconstructed subclonal phylogenetic trees by manual expert curation, we show how different configurations of our tools can

  18. Evolutionary Information Theory

    OpenAIRE

    Mark Burgin

    2013-01-01

    Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we const...

  19. Evolutionary developmental psychology

    National Research Council Canada - National Science Library

    King, Ashley C; Bjorklund, David F

    2010-01-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection...

  20. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.

    Science.gov (United States)

    Yi, Xuan; Gao, Lei; Wang, Bo; Su, Ying-Juan; Wang, Ting

    2013-01-01

    We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

  1. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

    Directory of Open Access Journals (Sweden)

    Holt Robert A

    2010-04-01

    Full Text Available Abstract Background Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (Salmo salar, but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution. Results From existing expressed sequence tag (EST resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (Esox lucius ESTs. Pairwise dN/dS comparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates. Conclusions 9,057 full-length reference genes were characterized in S. salar and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.

  2. Complete genomic sequence analyses of the first group A giraffe rotavirus reveals close evolutionary relationship with rotaviruses infecting other members of the Artiodactyla.

    Science.gov (United States)

    O'Shea, Helen; Mulherin, Emily; Matthijnssens, Jelle; McCusker, Matthew P; Collins, P J; Cashman, Olivia; Gunn, Lynda; Beltman, Marijke E; Fanning, Séamus

    2014-05-14

    Group A Rotaviruses (RVA) have been established as significant contributory agents of acute gastroenteritis in young children and many animal species. In 2008, we described the first RVA strain detected in a giraffe calf (RVA/Giraffe-wt/IRL/GirRV/2008/G10P[11]), presenting with acute diarrhoea. Molecular characterisation of the VP7 and VP4 genes revealed the bovine-like genotypes G10 and P[11], respectively. To further investigate the origin of this giraffe RVA strain, the 9 remaining gene segments were sequenced and analysed, revealing the following genotype constellation: G10-P[11]-I2-R2-C2-M2-A3-N2-T6-E2-H3. This genotype constellation is very similar to RVA strains isolated from cattle or other members of the artiodactyls. Phylogenetic analyses confirmed the close relationship between GirRV and RVA strains with a bovine-like genotype constellation detected from several host species, including humans. These results suggest that RVA strain GirRV was the result of an interspecies transmission from a bovine host to the giraffe calf. However, we cannot rule out completely that this bovine-like RVA genotype constellation may be enzootic in giraffes. Future RVA surveillance in giraffes may answer this intriguing question.

  3. Molecular comparison and evolutionary analyses of VP1 nucleotide sequences of new African human enterovirus 71 isolates reveal a wide genetic diversity.

    Directory of Open Access Journals (Sweden)

    Maël Bessaud

    Full Text Available Most circulating strains of Human enterovirus 71 (EV-A71 have been classified primarily into three genogroups (A to C on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D and 2 African ones (E and F. Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied.

  4. Evolutionary changes in gene expression, coding sequence and copy-number at the Cyp6g1 locus contribute to resistance to multiple insecticides in Drosophila.

    Directory of Open Access Journals (Sweden)

    Thomas W R Harrop

    Full Text Available Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster-D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species.

  5. Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent ▿ †

    Science.gov (United States)

    Vinuesa, Pablo; Rojas-Jiménez, Keilor; Contreras-Moreira, Bruno; Mahna, Suresh K.; Prasad, Braj Nandan; Moe, Hla; Selvaraju, Suresh Babu; Thierfelder, Heidemarie; Werner, Dietrich

    2008-01-01

    A highly supported maximum-likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix obtained from the concatenation of partial atpD, recA, glnII, and rpoB sequences corresponding to 33 reference strains and 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from Myanmar, India, Nepal, and Vietnam. The power of the multigene approach using multiple strains per species was evaluated in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial molecular systematics. Potential pitfalls of the approach are highlighted. Seventy-five of the isolates could be classified as B. japonicum type Ia (USDA110/USDA122-like), B. liaoningense, B. yuanmingense, or B. elkanii, whereas one represented a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related to strain USDA110. Significant phylogenetic evidence against the monophyly of the of B. japonicum I and Ia lineages was found. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation, and contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by mapping climate types and geographic origins of the isolates on the species tree. PMID:18791003

  6. Evolutionary Information Theory

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2013-04-01

    Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.

  7. BEAST: Bayesian evolutionary analysis by sampling trees

    Directory of Open Access Journals (Sweden)

    Drummond Alexei J

    2007-11-01

    Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

  8. Evolutionary genetics of insect innate immunity

    OpenAIRE

    Viljakainen, Lumi

    2015-01-01

    Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on g...

  9. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  10. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  11. Evolutionary genetics of insect innate immunity.

    Science.gov (United States)

    Viljakainen, Lumi

    2015-11-01

    Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered. © The Author 2015. Published by Oxford University Press.

  12. The Evolutionary Chromosome Translocation 4;19 in Gorilla gorilla is Associated with Microduplication of the Chromosome Fragment Syntenic to Sequences Surrounding the Human Proximal CMT1A-REP

    OpenAIRE

    Stankiewicz, Pawel; Park, Sung-Sup; Inoue, Ken; Lupski, James R.

    2001-01-01

    Many genomic disorders occur as a result of chromosome rearrangements involving low-copy repeats (LCRs). To better understand the molecular basis of chromosome rearrangements, including translocations, we have investigated the mechanism of evolutionary rearrangements. In contrast to several intrachromosomal rearrangements, only two evolutionary translocations have been identified by cytogenetic analyses of humans and greater apes. Human chromosome 2 arose as a result of a telomeric fusion bet...

  13. Evolutionary Phylogenetic Networks: Models and Issues

    Science.gov (United States)

    Nakhleh, Luay

    Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of non-treelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many cases, have propelled research and interest in phylogenetic networks to the forefront in computational phylogenetics. Nonetheless, the term 'phylogenetic network' has been generically used to refer to a class of models whose core shared property is tree generalization. Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently. However, unlike these surveys, this chapte focuses specifically on one type of phylogenetic networks, namely evolutionary phylogenetic networks, which explicitly model reticulate evolutionary events. Further, this chapter focuses less on surveying existing tools, and addresses in more detail issues that are central to the accurate reconstruction of phylogenetic networks.

  14. Remembering the evolutionary Freud.

    Science.gov (United States)

    Young, Allan

    2006-03-01

    Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.

  15. Evolutionary shaping of demographic schedules

    Science.gov (United States)

    Wachter, Kenneth W.; Steinsaltz, David; Evans, Steven N.

    2014-01-01

    Evolutionary processes of natural selection may be expected to leave their mark on age patterns of survival and reproduction. Demographic theory includes three main strands—mutation accumulation, stochastic vitality, and optimal life histories. This paper reviews the three strands and, concentrating on mutation accumulation, extends a mathematical result with broad implications concerning the effect of interactions between small age-specific effects of deleterious mutant alleles. Empirical data from genomic sequencing along with prospects for combining strands of theory hold hope for future progress. PMID:25024186

  16. Ernst Haeckel's concept of an evolutionary origin of life.

    Science.gov (United States)

    Dose, K

    1981-01-01

    In 1865/66 E. Haeckel for the first time suggested an evolutionary sequence in order to explain the origin of the first living cell. Haeckel's concept is compared with modern theories of the origin of life. It is evident that Haeckel has not as yet received the credit that he deserves for his evolutionary concept.

  17. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

    Science.gov (United States)

    Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

    2012-01-01

    Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.

  18. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  19. A Clustal Alignment Improver Using Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Thomsen, Rene; Fogel, Gary B.; Krink, Thimo

    2002-01-01

    Multiple sequence alignment (MSA) is a crucial task in bioinformatics. In this paper we extended previous work with evolutionary algorithms (EA) by using MSA solutions obtained from the wellknown Clustal V algorithm as a candidate solution seed of the initial EA population. Our results clearly show...

  20. Evolutionary humanoid robotics

    CERN Document Server

    Eaton, Malachy

    2015-01-01

    This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.

  1. Evolutionary plasticity of insect immunity.

    Science.gov (United States)

    Vilcinskas, Andreas

    2013-02-01

    Many insect genomes have been sequenced and the innate immune responses of several species have been studied by transcriptomics, inviting the comparative analysis of immunity-related genes. Such studies have demonstrated significant evolutionary plasticity, with the emergence of novel proteins and protein domains correlated with insects adapting to both abiotic and biotic environmental stresses. This review article focuses on effector molecules such as antimicrobial peptides (AMPs) and proteinase inhibitors, which display greater evolutionary dynamism than conserved components such as immunity-related signaling molecules. There is increasing evidence to support an extended role for insect AMPs beyond defense against pathogens, including the management of beneficial endosymbionts. The total number of AMPs varies among insects with completed genome sequences, providing intriguing examples of immunity gene expansion and loss. This plasticity is discussed in the context of recent developments in evolutionary ecology suggesting that the maintenance and deployment of immune responses reallocates resources from other fitness-related traits thus requiring fitness trade-offs. Based on our recent studies using both model and non-model insects, I propose that insect immunity genes can be lost when alternative defense strategies with a lower fitness penalty have evolved, such as the so-called social immunity in bees, the chemical sanitation of the microenvironment by some beetles, and the release of antimicrobial secondary metabolites in the hemolymph. Conversely, recent studies provide evidence for the expansion and functional diversification of insect AMPs and proteinase inhibitors to reflect coevolution with a changing pathosphere and/or adaptations to habitats or food associated with microbial contamination. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. PARSEC evolutionary tracks of massive stars up to $350 M_\\odot$ at metallicities 0.0001$\\leq Z \\leq$0.04

    CERN Document Server

    Chen, Yang; Girardi, Léo; Marigo, Paola; Kong, Xu; Lanza, Antonio

    2015-01-01

    We complement the PARSEC database of stellar evolutionary tracks with new models of massive stars, from the pre-main sequence phase to the central carbon ignition. We consider a broad range of metallicities, 0.0001$\\leq Z \\leq$0.04 and initial masses up to $M_{\\rm ini}=350\\,M_\\odot$. The main difference with respect to our previous models of massive stars is the adoption of a recent formalism accounting for the mass-loss enhancement when the ratio of the stellar to the Eddington luminosity, $\\Gamma_e$, approaches unity. With this new formalism, the models are able to reproduce the Humphreys-Davidson limit observed in the Galactic and LMC colour-magnitude diagrams, without an ad hoc mass-loss enhancement. We also follow the predictions of recent wind models indicating that the metallicity dependence of the mass-loss rates becomes shallower when $\\Gamma_e$ approaches unity. We thus find that the more massive stars may suffer from substantial mass-loss even at low metallicity. We also predict that the Humphreys-...

  3. Analyses on the types of copy and evolutionary relationships of ITS sequence of Phormidium%席藻 ITS 序列拷贝类型及进化关系分析

    Institute of Scientific and Technical Information of China (English)

    焦淑静; 黄现恩; 谷青; 史全良

    2014-01-01

    The coevolution of the ITS sequences hasn't been fully accomplished leading to multiple types of copy in cy-anobacteria,while the distribution rule of ITS copy in cyanobacteria are unclear.We used Phormidium strains picked up from Suzhou districts and 12 other strains selected from Genebank as the materials to study the characteristics and the evolutionary relationships among different types of copy.The results showed that the PCR product of ITS of Phormidium had single band (i.e.ITS-IA type or ITS-I type)or two bands(i.e.ITS-IA and ITS-N type),and ITS-IA was the most popular type in the materials used in this study;the phylogeny analyzed results indicated that ITS-IA type and ITS-I type were distributed in different groups respectively,and the ITS-IA group appeared earlier than ITS-I group.Thus we proved that ITS-I type was evolved from a deletion of tRNAAla coding region of ITS-IA type, and ITS-IA type should be the basic structure of ITS copy of Phormidium .%由于协同进化未完成,蓝藻的16S-23S rDNA 基因间隔序列(ITS)存在多种拷贝类型,目前蓝藻 ITS序列的拷贝类型分布以及演化规律尚未研究清楚。该文采用本地采集的席藻属样品,测定其 ITS 序列,并结合基因库中已有的席藻 ITS 序列,对席藻属蓝藻 ITS 序列拷贝类型及其之间的进化关系进行探讨。结果显示,席藻属 ITS 序列的 PCR 产物有两种情况,即单一条带(仅出现 ITS-IA 或 ITS-I 型)和两条条带(同时出现ITS-IA 和 ITS-N 型),其中以单一条带的 ITS-IA 型最为普遍;在基于 ITS 序列的系统发生树中,ITS-IA 型和ITS-I 型均各自聚为一个组群,且 ITS-IA 型的组群节点出现较早,表明席藻属 ITS-I 型极有可能是由其原来的 ITS-IA 型缺失 tRNAAla编码区进化而来,ITS-IA 型应为席藻 ITS 序列的基本结构。

  4. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  5. Part E: Evolutionary Computation

    DEFF Research Database (Denmark)

    2015-01-01

    of Computational Intelligence. First, comprehensive surveys of genetic algorithms, genetic programming, evolution strategies, parallel evolutionary algorithms are presented, which are readable and constructive so that a large audience might find them useful and – to some extent – ready to use. Some more general...... topics like the estimation of distribution algorithms, indicator-based selection, etc., are also discussed. An important problem, from a theoretical and practical point of view, of learning classifier systems is presented in depth. Multiobjective evolutionary algorithms, which constitute one of the most...... evolutionary algorithms, such as memetic algorithms, which have emerged as a very promising tool for solving many real-world problems in a multitude of areas of science and technology. Moreover, parallel evolutionary combinatorial optimization has been presented. Search operators, which are crucial in all...

  6. Evolutionary mechanisms for loneliness.

    Science.gov (United States)

    Cacioppo, John T; Cacioppo, Stephanie; Boomsma, Dorret I

    2014-01-01

    Robert Weiss (1973) conceptualised loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organisation than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale.

  7. Rethinking evolutionary individuality.

    Science.gov (United States)

    Ereshefsky, Marc; Pedroso, Makmiller

    2015-08-18

    This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed.

  8. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-01

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

  9. PARSEC evolutionary tracks of massive stars up to 350 M⊙ at metallicities 0.0001 ≤ Z ≤ 0.04

    Science.gov (United States)

    Chen, Yang; Bressan, Alessandro; Girardi, Léo; Marigo, Paola; Kong, Xu; Lanza, Antonio

    2015-09-01

    We complement the PARSEC data base of stellar evolutionary tracks with new models of massive stars, from the pre-main-sequence phase to the central carbon ignition. We consider a broad range of metallicities, 0.0001 ≤ Z ≤ 0.04 and initial masses up to Mini = 350 M⊙. The main difference with respect to our previous models of massive stars is the adoption of a recent formalizm accounting for the mass-loss enhancement when the ratio of the stellar to the Eddington luminosity, Γe, approaches unity. With this new formalizm, the models are able to reproduce the Humphreys-Davidson limit observed in the Galactic and Large Magellanic Cloud colour-magnitude diagrams, without an ad hoc mass-loss enhancement. We also follow the predictions of recent wind models indicating that the metallicity dependence of the mass-loss rates becomes shallower when Γe approaches unity. We thus find that the more massive stars may suffer from substantial mass-loss even at low metallicity. We also predict that the Humphreys-Davidson limit should become brighter at decreasing metallicity. We supplement the evolutionary tracks with new tables of theoretical bolometric corrections, useful to compare tracks and isochrones with the observations. For this purpose, we homogenize existing stellar atmosphere libraries of hot and cool stars (Potsdam Wolf-Rayet, ATLAS9 and PHOENIX) and we add, where needed, new atmosphere models computed with WM-BASIC. The mass, age and metallicity grids are fully adequate to perform detailed investigations of the properties of very young stellar systems, both in local and distant galaxies. The new tracks supersede the previous old PADOVA models of massive stars.

  10. Autonomous Evolutionary Information Systems

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Traditional information systems are passive, i.e., data orknowledge is created , retrieved, modified, updated, and deleted only in response to operations issued by users or application programs, and the systems only can execute queries or t ransactions explicitly submitted by users or application programs but have no ab ility to do something actively by themselves. Unlike a traditional information system serving just as a storehouse of data or knowledge and working passively a ccording to queries or transactions explicitly issued by users and application p rograms, an autonomous evolutionary information system serves as an autonomous a nd evolutionary partner of its users that discovers new knowledge from its datab ase or knowledge-base autonomously, cooperates with its users in solving proble m s actively by providing the users with advices, and has a certain mechanism to i mprove its own state of “knowing” and ability of “working”. This paper semi nall y defines what is an autonomous evolutionary information system, explain why aut onomous evolutionary information systems are needed, and presents some new issue s, fundamental considerations, and research directions in design and development of autonomous evolutionary information systems.

  11. Applying evolutionary anthropology.

    Science.gov (United States)

    Gibson, Mhairi A; Lawson, David W

    2015-01-01

    Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. © 2015 Wiley Periodicals, Inc.

  12. Paleoanthropology and evolutionary theory.

    Science.gov (United States)

    Tattersall, Ian

    2012-01-01

    Paleoanthropologists of the first half of the twentieth century were little concerned either with evolutionary theory or with the technicalities and broader implications of zoological nomenclature. In consequence, the paleoanthropological literature of the period consisted largely of a series of descriptions accompanied by authoritative pronouncements, together with a huge excess of hominid genera and species. Given the intellectual flimsiness of the resulting paleoanthropological framework, it is hardly surprising that in 1950 the ornithologist Ernst Mayr met little resistance when he urged the new postwar generation of paleoanthropologists to accept not only the elegant reductionism of the Evolutionary Synthesis but a vast oversimplification of hominid phylogenetic history and nomenclature. Indeed, the impact of Mayr's onslaught was so great that even when developments in evolutionary biology during the last quarter of the century brought other paleontologists to the realization that much more has been involved in evolutionary histories than the simple action of natural selection within gradually transforming lineages, paleoanthropologists proved highly reluctant to follow. Even today, paleoanthropologists are struggling to reconcile an intuitive realization that the burgeoning hominid fossil record harbors a substantial diversity of species (bringing hominid evolutionary patterns into line with that of other successful mammalian families), with the desire to cram a huge variety of morphologies into an unrealistically minimalist systematic framework. As long as this theoretical ambivalence persists, our perception of events in hominid phylogeny will continue to be distorted.

  13. Evolutionary origins of membrane proteins

    Science.gov (United States)

    Mulkidjanian, Armen Y.; Galperin, Michael Y.

    Although the genes that encode membrane proteins make about 30% of the sequenced genomes, the evolution of membrane proteins and their origins are still poorly understood. Here we address this topic by taking a closer look at those membrane proteins the ancestors of which were present in the Last Universal Common Ancestor, and in particular, the F/V-type rotating ATPases. Reconstruction of their evolutionary history provides hints for understanding not only the origin of membrane proteins, but also of membranes themselves. We argue that the evolution of biological membranes could occur as a process of coevolution of lipid bilayers and membrane proteins, where the increase in the ion-tightness of the membrane bilayer may have been accompanied by a transition from amphiphilic, pore-forming membrane proteins to highly hydrophobic integral membrane complexes.

  14. Evolutionary adaptations to dietary changes.

    Science.gov (United States)

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.

  15. The Ancient Evolutionary History of Polyomaviruses.

    Directory of Open Access Journals (Sweden)

    Christopher B Buck

    2016-04-01

    Full Text Available Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.

  16. The Ancient Evolutionary History of Polyomaviruses

    Science.gov (United States)

    Buck, Christopher B.; Van Doorslaer, Koenraad; Peretti, Alberto; Geoghegan, Eileen M.; Tisza, Michael J.; An, Ping; Katz, Joshua P.; Pipas, James M.; McBride, Alison A.; Camus, Alvin C.; McDermott, Alexa J.; Dill, Jennifer A.; Delwart, Eric; Ng, Terry F. F.; Farkas, Kata; Austin, Charlotte; Kraberger, Simona; Davison, William; Pastrana, Diana V.; Varsani, Arvind

    2016-01-01

    Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. PMID:27093155

  17. The Use of Evolutionary Approaches to Understand Single Cell Genomes

    Directory of Open Access Journals (Sweden)

    Haiwei eLuo

    2015-03-01

    Full Text Available The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.

  18. Evolutionary Computation:ao Overview

    Institute of Scientific and Technical Information of China (English)

    HeZhenya; WeiChengjian

    1997-01-01

    Evolutionary computation is a field of simulating evolution on a computer.Both aspects of it ,the problem solving aspect and the aspect of modeling natural evolution,are important.Simulating evolution on a computer results in stochastic optimization techniques that can outperform classical methods of optimization when applied to difficult real-world problems.There are currently four main avenues of research in simulated evolution:genetic algorithms,evolutionary programming,evolution strategies,and genetic programming.This paper presents a brief overview of thd field on evolutionary computation,including some theoretical issues,adaptive mechanisms,improvements,constrained optimizqtion,constrained satisfaction,evolutionary neural networks,evolutionary fuzzy systems,hardware evolution,evolutionary robotics,parallel evolutionary computation,and co-evolutionary models.The applications of evolutionary computation for optimizing system and intelligent information processing in telecommunications are also introduced.

  19. Evolutionary Design in Art

    Science.gov (United States)

    McCormack, Jon

    Evolution is one of the most interesting and creative processes we currently understand, so it should come as no surprise that artists and designers are embracing the use of evolution in problems of artistic creativity. The material in this section illustrates the diversity of approaches being used by artists and designers in relation to evolution at the boundary of art and science. While conceptualising human creativity as an evolutionary process in itself may be controversial, what is clear is that evolutionary processes can be used to complement, even enhance human creativity, as the chapters in this section aptly demonstrate.

  20. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    Darwinian evolution by natural selection is driven primarily by differential survival and reproduction among individuals in a population. When the evolutionary interest of an individual is in conflict with the interests of the population, the genes increasing individual fitness at the cost...... of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  1. Evolutionary Statistical Procedures

    CERN Document Server

    Baragona, Roberto; Poli, Irene

    2011-01-01

    This proposed text appears to be a good introduction to evolutionary computation for use in applied statistics research. The authors draw from a vast base of knowledge about the current literature in both the design of evolutionary algorithms and statistical techniques. Modern statistical research is on the threshold of solving increasingly complex problems in high dimensions, and the generalization of its methodology to parameters whose estimators do not follow mathematically simple distributions is underway. Many of these challenges involve optimizing functions for which analytic solutions a

  2. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  3. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Graziele Pereira Oliveira

    2017-01-01

    Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.

  4. Synonymous genes explore different evolutionary landscapes.

    Directory of Open Access Journals (Sweden)

    Guillaume Cambray

    2008-11-01

    Full Text Available The evolutionary potential of a gene is constrained not only by the amino acid sequence of its product, but by its DNA sequence as well. The topology of the genetic code is such that half of the amino acids exhibit synonymous codons that can reach different subsets of amino acids from each other through single mutation. Thus, synonymous DNA sequences should access different regions of the protein sequence space through a limited number of mutations, and this may deeply influence the evolution of natural proteins. Here, we demonstrate that this feature can be of value for manipulating protein evolvability. We designed an algorithm that, starting from an input gene, constructs a synonymous sequence that systematically includes the codons with the most different evolutionary perspectives; i.e., codons that maximize accessibility to amino acids previously unreachable from the template by point mutation. A synonymous version of a bacterial antibiotic resistance gene was computed and synthesized. When concurrently submitted to identical directed evolution protocols, both the wild type and the recoded sequence led to the isolation of specific, advantageous phenotypic variants. Simulations based on a mutation isolated only from the synthetic gene libraries were conducted to assess the impact of sub-functional selective constraints, such as codon usage, on natural adaptation. Our data demonstrate that rational design of synonymous synthetic genes stands as an affordable improvement to any directed evolution protocol. We show that using two synonymous DNA sequences improves the overall yield of the procedure by increasing the diversity of mutants generated. These results provide conclusive evidence that synonymous coding sequences do experience different areas of the corresponding protein adaptive landscape, and that a sequence's codon usage effectively constrains the evolution of the encoded protein.

  5. Evolutionary conservation of alternative splicing in chicken

    Science.gov (United States)

    Katyal, S.; Gao, Z.; Liu, R.-Z.; Godbout, R.

    2013-01-01

    Alternative splicing represents a source of great diversity for regulating protein expression and function. It has been estimated that one-third to two-thirds of mammalian genes are alternatively spliced. With the sequencing of the chicken genome and analysis of transcripts expressed in chicken tissues, we are now in a position to address evolutionary conservation of alternative splicing events in chicken and mammals. Here, we compare chicken and mammalian transcript sequences of 41 alternatively-spliced genes and 50 frequently accessed genes. Our results support a high frequency of splicing events in chicken, similar to that observed in mammals. PMID:17675855

  6. Origins of evolutionary transitions

    Indian Academy of Sciences (India)

    Ellen Clarke

    2014-04-01

    An `evolutionary transition in individuality’ or `major transition’ is a transformation in the hierarchical level at which natural selection operates on a population. In this article I give an abstract (i.e. level-neutral and substrate-neutral) articulation of the transition process in order to precisely understand how such processes can happen, especially how they can get started.

  7. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these

  8. Studies in evolutionary agroecology

    DEFF Research Database (Denmark)

    Wille, Wibke

    of Evolutionary Agroecology that the highest yielding individuals do not necessarily perform best as a population. The investment of resources into strategies and structures increasing individual competitive ability carries a cost. If a whole population consists of individuals investing resources to compete...

  9. Evolutionary developmental psychology.

    Science.gov (United States)

    King, Ashley C; Bjorklund, David F

    2010-02-01

    The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection with the study of human development, focusing on the epigenetic effects that occur between humans and their environment in a way that attempts to explain how evolved psychological mechanisms become expressed in the phenotypes of adults. An evolutionary developmental perspective includes an appreciation of comparative research and we, among others, argue that contrasting the cognition of humans with that of nonhuman primates can provide a framework with which to understand how human cognitive abilities and intelligence evolved. Furthermore, we argue that several aspects of childhood (e.g., play and immature cognition) serve both as deferred adaptations as well as imparting immediate benefits. Intense selection pressure was surely exerted on childhood over human evolutionary history and, as a result, neglecting to consider the early developmental period of children when studying their later adulthood produces an incomplete picture of the evolved adaptations expressed through human behavior and cognition.

  10. Optimal Mixing Evolutionary Algorithms

    NARCIS (Netherlands)

    Thierens, D.; Bosman, P.A.N.; Krasnogor, N.

    2011-01-01

    A key search mechanism in Evolutionary Algorithms is the mixing or juxtaposing of partial solutions present in the parent solutions. In this paper we look at the efficiency of mixing in genetic algorithms (GAs) and estimation-of-distribution algorithms (EDAs). We compute the mixing probabilities of

  11. Evolutionary perspectives on ageing.

    Science.gov (United States)

    Reichard, Martin

    2017-05-26

    From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Evolutionary Theories of Detection

    Energy Technology Data Exchange (ETDEWEB)

    Fitch, J P

    2005-04-29

    Current, mid-term and long range technologies for detection of pathogens and toxins are briefly described in the context of performance metrics and operational scenarios. Predictive (evolutionary) and speculative (revolutionary) assessments are given with trade-offs identified, where possible, among competing performance goals.

  13. Evolutionary trends in Heteroptera

    NARCIS (Netherlands)

    Cobben, R.H.

    1968-01-01

    1. This work, the first volume of a series dealing with evolutionary trends in Heteroptera, is concerned with the egg system of about 400 species. The data are presented systematically in chapters 1 and 2 with a critical review of the literature after each family.

    2. Chapter 3 evaluates facts

  14. Learning: An Evolutionary Analysis

    Science.gov (United States)

    Swann, Joanna

    2009-01-01

    This paper draws on the philosophy of Karl Popper to present a descriptive evolutionary epistemology that offers philosophical solutions to the following related problems: "What happens when learning takes place?" and "What happens in human learning?" It provides a detailed analysis of how learning takes place without any direct transfer of…

  15. Evolutionary mysteries in meiosis

    NARCIS (Netherlands)

    Lenormand, Thomas; Engelstädter, Jan; Johnston, Susan E.; Wijnker, Erik; Haag, Christoph R.

    2016-01-01

    Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these o

  16. [Schizophrenia and evolutionary psychopathology].

    Science.gov (United States)

    Kelemen, Oguz; Kéri, Szabolcs

    2007-01-01

    Evolution can shape any characteristic appearing as a phenotype that is genetically rooted and possesses a long history. The stress-diathesis model suggests that psychiatric disorders have some genetic roots, and therefore the theory of evolution may be relevant for psychiatry. Schizophrenia is present in every human culture with approximately the same incidence. The great evolutionary paradox is: how can such illness persist despite fundamental reproductive disadvantages? Since the 1960s, several evolutionary explanations have been raised to explain the origins of schizophrenia. This article reviews all the major evolutionary theories about the possible origins of this disease. On the one hand, some researchers have proposed that schizophrenia is an evolutionary disadvantageous byproduct of human brain evolution (e.g. the evolution of hemispheric specialization, social brain or language skills). On the other hand, others have suggested that a compensatory advantage must exist either in the biological system of patients with schizophrenia (e.g. resistance against infectious diseases), or within the social domain (e.g. greater creativity of the relatives). According to some theories, shamanism and religion demonstrate some similarities to psychosis and provide clues regarding the origins of schizophrenia. At the end of this article we discuss this last theory in detail listing arguments for and against.

  17. Molluscan Evolutionary Development

    DEFF Research Database (Denmark)

    Wanninger, Andreas Wilhelm Georg; Koop, Damien; Moshel-Lynch, Sharon

    2008-01-01

    Brought together by Winston F. Ponder and David R. Lindberg, thirty-six experts on the evolution of the Mollusca provide an up-to-date review of its evolutionary history. The Mollusca are the second largest animal phylum and boast a fossil record of over 540 million years. They exhibit remarkable...

  18. When development matters: From evolutionary psychology to evolutionary developmental psychology

    OpenAIRE

    Hernández Blasi, Carlos; Gardiner, Amy K.; David F. Bjorklund

    2008-01-01

    This article presents evolutionary developmental psychology (EDP) as an emerging field of evolutionary psychology (EP). In describing the core tenets of both approaches and the differences between them, we emphasize the important roles that evolution and development have in understanding human behaviour. We suggest that developmental psychologists should pay more attention to evolutionary issues and, conversely, evolutionary psychologists should take development seriously. Key words: evol...

  19. Recent Advances in Evolutionary Computation

    Institute of Scientific and Technical Information of China (English)

    Xin Yao; Yong Xu

    2006-01-01

    Evolutionary computation has experienced a tremendous growth in the last decade in both theoretical analyses and industrial applications. Its scope has evolved beyond its original meaning of "biological evolution" toward a wide variety of nature inspired computational algorithms and techniques, including evolutionary, neural, ecological, social and economical computation, etc., in a unified framework. Many research topics in evolutionary computation nowadays are not necessarily "evolutionary". This paper provides an overview of some recent advances in evolutionary computation that have been made in CERCIA at the University of Birmingham, UK. It covers a wide range of topics in optimization, learning and design using evolutionary approaches and techniques, and theoretical results in the computational time complexity of evolutionary algorithms. Some issues related to future development of evolutionary computation are also discussed.

  20. Evolutionary history of exon shuffling.

    Science.gov (United States)

    França, Gustavo S; Cancherini, Douglas V; de Souza, Sandro J

    2012-06-01

    Exon shuffling has been characterized as one of the major evolutionary forces shaping both the genome and the proteome of eukaryotes. This mechanism was particularly important in the creation of multidomain proteins during animal evolution, bringing a number of functional genetic novelties. Here, genome information from a variety of eukaryotic species was used to address several issues related to the evolutionary history of exon shuffling. By comparing all protein sequences within each species, we were able to characterize exon shuffling signatures throughout metazoans. Intron phase (the position of the intron regarding the codon) and exon symmetry (the pattern of flanking introns for a given exon or block of adjacent exons) were features used to evaluate exon shuffling. We confirmed previous observations that exon shuffling mediated by phase 1 introns (1-1 exon shuffling) is the predominant kind in multicellular animals. Evidence is provided that such pattern was achieved since the early steps of animal evolution, supported by a detectable presence of 1-1 shuffling units in Trichoplax adhaerens and a considerable prevalence of them in Nematostella vectensis. In contrast, Monosiga brevicollis, one of the closest relatives of metazoans, and Arabidopsis thaliana, showed no evidence of 1-1 exon or domain shuffling above what it would be expected by chance. Instead, exon shuffling events are less abundant and predominantly mediated by phase 0 introns (0-0 exon shuffling) in those non-metazoan species. Moreover, an intermediate pattern of 1-1 and 0-0 exon shuffling was observed for the placozoan T. adhaerens, a primitive animal. Finally, characterization of flanking intron phases around domain borders allowed us to identify a common set of symmetric 1-1 domains that have been shuffled throughout the metazoan lineage.

  1. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  2. Evolutionary status of Entamoeba

    Institute of Scientific and Technical Information of China (English)

    DONG Jiuhong; WEN Jianfan; XIN Dedong; LU Siqi

    2004-01-01

    In addition to its medical importance as parasitic pathogen, Entamoeba has aroused people's interest in its evolutionary status for a long time. Lacking mitochondrion and other intracellular organelles common to typical eukaryotes, Entamoeba and several other amitochondrial protozoans have been recognized as ancient pre-mitochondriate eukaryotes and named "archezoa", the most primitive extant eukaryotes. It was suggested that they might be living fossils that remained in a primitive stage of evolution before acquisition of organelles, lying close to the transition between prokaryotes and eukaryotes. However, recent studies revealed that Entamoeba contained an organelle, "crypton" or "mitosome", which was regarded as specialized or reductive mitochondrion. Relative molecular phylogenetic analyses also indicated the existence or the probable existence of mitochondrion in Entamoeba. Our phylogenetic analysis based on DNA topoisomerase II strongly suggested its divergence after some mitchondriate eukaryotes. Here, all these recent researches are reviewed and the evolutionary status of Entamoeba is discussed.

  3. Evolutionary internalized regularities.

    Science.gov (United States)

    Schwartz, R

    2001-08-01

    Roger Shepard's proposals and supporting experiments concerning evolutionary internalized regularities have been very influential in the study of vision and in other areas of psychology and cognitive science. This paper examines issues concerning the need, nature, explanatory role, and justification for postulating such internalized constraints. In particular, I seek further clarification from Shepard on how best to understand his claim that principles of kinematic geometry underlie phenomena of motion perception. My primary focus is on the ecological validity of Shepard's kinematic constraint in the context of ordinary motion perception. First, I explore the analogy Shepard draws between internalized circadian rhythms and the supposed internalization of kinematic geometry. Next, questions are raised about how to interpret and justify applying results from his own and others' experimental studies of apparent motion to more everyday cases of motion perception in richer environments. Finally, some difficulties with Shepard's account of the evolutionary development of his kinematic constraint are considered.

  4. Evolutionary biology of cancer.

    Science.gov (United States)

    Crespi, Bernard; Summers, Kyle

    2005-10-01

    Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.

  5. Evolutionary game design

    CERN Document Server

    Browne, Cameron

    2011-01-01

    The book describes the world's first successful experiment in fully automated board game design. Evolutionary methods were used to derive new rule sets within a custom game description language, and self-play trials used to estimate each derived game's potential to interest human players. The end result is a number of new and interesting games, one of which has proved popular and gone on to be commercially published.

  6. Evolutionary theory of cancer.

    Science.gov (United States)

    Attolini, Camille Stephan-Otto; Michor, Franziska

    2009-06-01

    As Theodosius Dobzhansky famously noted in 1973, "Nothing in biology makes sense except in the light of evolution," and cancer is no exception to this rule. Our understanding of cancer initiation, progression, treatment, and resistance has advanced considerably by regarding cancer as the product of evolutionary processes. Here we review the literature of mathematical models of cancer evolution and provide a synthesis and discussion of the field.

  7. Asymmetric Evolutionary Games.

    Directory of Open Access Journals (Sweden)

    Alex McAvoy

    2015-08-01

    Full Text Available Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games.

  8. Modified evolutionary algorithm for global optimization

    Institute of Scientific and Technical Information of China (English)

    郭崇慧; 陆玉昌; 唐焕文

    2004-01-01

    A modification of evolutionary programming or evolution strategies for n-dimensional global optimization is proposed. Based on the ergodicity and inherent-randomness of chaos, the main characteristic of the new algorithm which includes two phases is that chaotic behavior is exploited to conduct a rough search of the problem space in order to find the promising individuals in Phase Ⅰ. Adjustment strategy of step-length and intensive searches in Phase Ⅱ are employed.The population sequences generated by the algorithm asymptotically converge to global optimal solutions with probability one. The proposed algorithm is applied to several typical test problems. Numerical results illustrate that this algorithm can more efficiently solve complex global optimization problems than evolutionary programming and evolution strategies in most cases.

  9. MELEC: Meta-Level Evolutionary Composer

    Directory of Open Access Journals (Sweden)

    Andres Calvo

    2011-02-01

    Full Text Available Genetic algorithms (GA’s are global search mechanisms that have been applied to many disciplines including music composition. Computer system MELEC composes music using evolutionary computation on two levels: the object and the meta. At the object-level, MELEC employs GAs to compose melodic motifs and iteratively refine them through evolving generations. At the meta-level, MELEC forms the overall musical structure by concatenating the generated motifs in an order that depends on the evolutionary process. In other words, the structure of the music is determined by a geneological traversal of the algorithm’s execution sequence. In this implementation, we introduce a new data structure that tracks the execution of the GA, the Genetic Algorithm Traversal Tree, and uses its traversal to define the musical structure. Moreover, we employ a Fibonacci-based fitness function to shape the melodic evolution.

  10. Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences.

    Science.gov (United States)

    Pombert, Jean-François; Sistek, Viridiana; Boissinot, Maurice; Frenette, Michel

    2009-10-30

    Streptococci are divided into six phylogenetic groups, i.e, anginosus, bovis, mitis, mutans, pyogenic, and salivarius, with the salivarius group consisting of only three distinct species. Two of these species, Streptococcus salivarius and Streptococcus vestibularis, are members of the normal human oral microflora whereas the third, Streptococcus thermophilus, is found in bovine milk. Given that S. salivarius and S. vestibularis share several physiological characteristics, in addition to inhabiting the same ecosystem, one would assume that they would be more closely related to each other than to S. thermophilus. However, the few phylogenetic trees published so far suggest that S. vestibularis is more closely related to S. thermophilus. To determine whether this phylogenetic relationship is genuine, we performed phylogenetic inferences derived from secA and secY, the general secretion housekeeping genes, recA, a gene from a separate genetic locus that encodes a major component of the homologous recombinational apparatus, and 16S rRNA-encoding gene sequences using other streptococcal species as outgroups. The maximum likelihood (ML) and maximum parsimony (MP) phylogenetic inferences derived from the secA and recA gene sequences provided strong support for the S. vestibularis/S. thermophilus sister-relationship, whereas 16S rRNA-encoding and secY-based analyses could not discriminate between alternate topologies. Phylogenetic analyses derived from the concatenation of these sequences unambiguously supported the close affiliation of S. vestibularis and S. thermophilus. Our results corroborated the sister-relationship between S. vestibularis and S. thermophilus and the concomitant early divergence of S. salivarius at the base of the salivarius lineage.

  11. Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences

    Directory of Open Access Journals (Sweden)

    Boissinot Maurice

    2009-10-01

    Full Text Available Abstract Background Streptococci are divided into six phylogenetic groups, i.e, anginosus, bovis, mitis, mutans, pyogenic, and salivarius, with the salivarius group consisting of only three distinct species. Two of these species, Streptococcus salivarius and Streptococcus vestibularis, are members of the normal human oral microflora whereas the third, Streptococcus thermophilus, is found in bovine milk. Given that S. salivarius and S. vestibularis share several physiological characteristics, in addition to inhabiting the same ecosystem, one would assume that they would be more closely related to each other than to S. thermophilus. However, the few phylogenetic trees published so far suggest that S. vestibularis is more closely related to S. thermophilus. To determine whether this phylogenetic relationship is genuine, we performed phylogenetic inferences derived from secA and secY, the general secretion housekeeping genes, recA, a gene from a separate genetic locus that encodes a major component of the homologous recombinational apparatus, and 16S rRNA-encoding gene sequences using other streptococcal species as outgroups. Results The maximum likelihood (ML and maximum parsimony (MP phylogenetic inferences derived from the secA and recA gene sequences provided strong support for the S. vestibularis/S. thermophilus sister-relationship, whereas 16S rRNA-encoding and secY-based analyses could not discriminate between alternate topologies. Phylogenetic analyses derived from the concatenation of these sequences unambiguously supported the close affiliation of S. vestibularis and S. thermophilus. Conclusion Our results corroborated the sister-relationship between S. vestibularis and S. thermophilus and the concomitant early divergence of S. salivarius at the base of the salivarius lineage.

  12. The evolutionary rate dynamically tracks changes in HIV-1 epidemics

    Energy Technology Data Exchange (ETDEWEB)

    Maljkovic-berry, Irina [Los Alamos National Laboratory; Athreya, Gayathri [Los Alamos National Laboratory; Daniels, Marcus [Los Alamos National Laboratory; Bruno, William [Los Alamos National Laboratory; Korber, Bette [Los Alamos National Laboratory; Kuiken, Carla [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory

    2009-01-01

    Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changed over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.

  13. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...... to the development of designs tailored to the individual preferences of inhabitants, changing the roles of architects and designers entirely. Architecture-as-it-could-be is a philosophical approach conducted through artistic methods to anticipate the technological futures of human-centered development within...

  14. Constraints as evolutionary systems

    CERN Document Server

    Rácz, István

    2016-01-01

    The constraint equations for smooth $[n+1]$-dimensional (with $n\\geq 3$) Riemannian or Lorentzian spaces satisfying the Einstein field equations are considered. It is shown, regardless of the signature of the primary space, that the constraints can be put into the form of an evolutionary system comprised either by a first order symmetric hyperbolic system and a parabolic equation or, alternatively, by a strongly hyperbolic system and a subsidiary algebraic relation. In both cases the (local) existence and uniqueness of solutions are also discussed.

  15. An evolutionary approach

    Science.gov (United States)

    Healy, Thomas J.

    1993-04-01

    The paper describes an evolutionary approach to the development of aerospace systems, represented by the introduction of integrated product teams (IPTs), which are now used at Rockwell's Space Systems Division on all new programs and are introduced into existing projects after demonstrations of increases in quality and reductions in cost and schedule due to IPTs. Each IPT is unique and reflects its own program and lasts for the life of the program. An IPT includes customers, suppliers, subcontractors, and associate contractors, and have a charter, mission, scope of authority, budget, and schedule. Functional management is responsible for the staffing, training, method development, and generic technology development.

  16. Distributed Evolutionary Graph Partitioning

    CERN Document Server

    Sanders, Peter

    2011-01-01

    We present a novel distributed evolutionary algorithm, KaFFPaE, to solve the Graph Partitioning Problem, which makes use of KaFFPa (Karlsruhe Fast Flow Partitioner). The use of our multilevel graph partitioner KaFFPa provides new effective crossover and mutation operators. By combining these with a scalable communication protocol we obtain a system that is able to improve the best known partitioning results for many inputs in a very short amount of time. For example, in Walshaw's well known benchmark tables we are able to improve or recompute 76% of entries for the tables with 1%, 3% and 5% imbalance.

  17. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  18. Evolutionary divergence of chloroplast FAD synthetase proteins

    Directory of Open Access Journals (Sweden)

    Arilla-Luna Sonia

    2010-10-01

    Full Text Available Abstract Background Flavin adenine dinucleotide synthetases (FADSs - a group of bifunctional enzymes that carry out the dual functions of riboflavin phosphorylation to produce flavin mononucleotide (FMN and its subsequent adenylation to generate FAD in most prokaryotes - were studied in plants in terms of sequence, structure and evolutionary history. Results Using a variety of bioinformatics methods we have found that FADS enzymes localized to the chloroplasts, which we term as plant-like FADS proteins, are distributed across a variety of green plant lineages and constitute a divergent protein family clearly of cyanobacterial origin. The C-terminal module of these enzymes does not contain the typical riboflavin kinase active site sequence, while the N-terminal module is broadly conserved. These results agree with a previous work reported by Sandoval et al. in 2008. Furthermore, our observations and preliminary experimental results indicate that the C-terminus of plant-like FADS proteins may contain a catalytic activity, but different to that of their prokaryotic counterparts. In fact, homology models predict that plant-specific conserved residues constitute a distinct active site in the C-terminus. Conclusions A structure-based sequence alignment and an in-depth evolutionary survey of FADS proteins, thought to be crucial in plant metabolism, are reported, which will be essential for the correct annotation of plant genomes and further structural and functional studies. This work is a contribution to our understanding of the evolutionary history of plant-like FADS enzymes, which constitute a new family of FADS proteins whose C-terminal module might be involved in a distinct catalytic activity.

  19. The evolutionary language game.

    Science.gov (United States)

    Nowak, M A; Plotkin, J B; Krakauer, D C

    1999-09-21

    We explore how evolutionary game dynamics have to be modified to accomodate a mathematical framework for the evolution of language. In particular, we are interested in the evolution of vocabulary, that is associations between signals and objects. We assume that successful communication contributes to biological fitness: individuals who communicate well leave more offspring. Children inherit from their parents a strategy for language learning (a language acquisition device). We consider three mechanisms whereby language is passed from one generation to the next: (i) parental learning: children learn the language of their parents; (ii) role model learning: children learn the language of individuals with a high payoff; and (iii) random learning: children learn the language of randomly chosen individuals. We show that parental and role model learning outperform random learning. Then we introduce mistakes in language learning and study how this process changes language over time. Mistakes increase the overall efficacy of parental and role model learning: in a world with errors evolutionary adaptation is more efficient. Our model also provides a simple explanation why homonomy is common while synonymy is rare. Copyright 1999 Academic Press.

  20. A comparison of evolutionary tracks for single Galactic massive stars

    CERN Document Server

    Martins, F

    2013-01-01

    In this paper, we compare the currently available evolutionary tracks for Galactic massive stars. Our main goal is to highlight the uncertainties on the predicted evolutionary paths. We compute stellar evolution models with the codes MESA and STAREVOL. We compare our results with those of four published grids of massive stellar evolution models (Geneva, STERN, Padova and FRANEC codes). We first investigate the effects of overshooting, mass loss, metallicity, chemical composition. We subsequently focus on rotation. Finally, we compare the predictions of published evolutionary models with the observed properties of a large sample of Galactic stars. We find that all models agree well for the main sequence evolution. Large differences in luminosity and temperatures appear for the post main sequence evolution, especially in the cool part of the HR diagram. Depending on the physical ingredients, tracks of different initial masses can overlap, rendering any mass estimate doubtful. For masses between 7 and 20 Msun, w...

  1. Protein Structure Prediction with Evolutionary Algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Hart, W.E.; Krasnogor, N.; Pelta, D.A.; Smith, J.

    1999-02-08

    Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the confirmational representation, the energy formulation and the way in which infeasible conformations are penalized, Further we empirically evaluated the impact of these factors on a small set of polymer sequences. Our analysis leads to specific recommendations for both GAs as well as other heuristic methods for solving PSP on the HP model.

  2. Using Evolutionary Data in Developing Phylogenetic Trees: A Scaffolded Approach with Authentic Data

    Science.gov (United States)

    Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

    2015-01-01

    Analyzing evolutionary relationships requires that students have a thorough understanding of evidence and of how scientists use evidence to develop these relationships. In this lesson sequence, students work in groups to process many different lines of evidence of evolutionary relationships between ungulates, then construct a scientific argument…

  3. Using Evolutionary Data in Developing Phylogenetic Trees: A Scaffolded Approach with Authentic Data

    Science.gov (United States)

    Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

    2015-01-01

    Analyzing evolutionary relationships requires that students have a thorough understanding of evidence and of how scientists use evidence to develop these relationships. In this lesson sequence, students work in groups to process many different lines of evidence of evolutionary relationships between ungulates, then construct a scientific argument…

  4. Grand challenges in evolutionary and population genetics: The importance of integrating epigenetics, genomics, modeling, and experimentation

    Science.gov (United States)

    Samuel A. Cushman

    2014-01-01

    This is a time of explosive growth in the fields of evolutionary and population genetics, with whole genome sequencing and bioinformatics driving a transformative paradigm shift (Morozova and Marra, 2008). At the same time, advances in epigenetics are thoroughly transforming our understanding of evolutionary processes and their implications for populations, species and...

  5. Evolutionary neurobiology and aesthetics.

    Science.gov (United States)

    Smith, Christopher Upham

    2005-01-01

    If aesthetics is a human universal, it should have a neurobiological basis. Although use of all the senses is, as Aristotle noted, pleasurable, the distance senses are primarily involved in aesthetics. The aesthetic response emerges from the central processing of sensory input. This occurs very rapidly, beneath the level of consciousness, and only the feeling of pleasure emerges into the conscious mind. This is exemplified by landscape appreciation, where it is suggested that a computation built into the nervous system during Paleolithic hunter-gathering is at work. Another inbuilt computation leading to an aesthetic response is the part-whole relationship. This, it is argued, may be traced to the predator-prey "arms races" of evolutionary history. Mate selection also may be responsible for part of our response to landscape and visual art. Aesthetics lies at the core of human mentality, and its study is consequently of importance not only to philosophers and art critics but also to neurobiologists.

  6. Spore: Spawning Evolutionary Misconceptions?

    Science.gov (United States)

    Bean, Thomas E.; Sinatra, Gale M.; Schrader, P. G.

    2010-10-01

    The use of computer simulations as educational tools may afford the means to develop understanding of evolution as a natural, emergent, and decentralized process. However, special consideration of developmental constraints on learning may be necessary when using these technologies. Specifically, the essentialist (biological forms possess an immutable essence), teleological (assignment of purpose to living things and/or parts of living things that may not be purposeful), and intentionality (assumption that events are caused by an intelligent agent) biases may be reinforced through the use of computer simulations, rather than addressed with instruction. We examine the video game Spore for its depiction of evolutionary content and its potential to reinforce these cognitive biases. In particular, we discuss three pedagogical strategies to mitigate weaknesses of Spore and other computer simulations: directly targeting misconceptions through refutational approaches, targeting specific principles of scientific inquiry, and directly addressing issues related to models as cognitive tools.

  7. Total Integrative Evolutionary Communication

    DEFF Research Database (Denmark)

    Nedergaard Thomsen, Ole; Brier, Søren

    2014-01-01

    ) instinctual-motivational-emotional sign plays (a level which is shared with other animals and is the domain of ethology), and (3) premeditated, intentional symbol-based language games (specifically human unitary thinking-speaking-gesturing, the domain of pragmatics-based functional linguistics......). In this inclusive hierarchy language games subsume the other stages, and thus human evolutionary communication is primarily a symbolic-conventional practice. It is intertwined with the practice of living, that is, with different life forms, including other forms of semiotic behavior. Together they form a coherent......In this paper we outline a cybersemiotic foundation for the trend of pragmatics-based functional linguistics, Functional Discourse Grammar. Cybersemiotics is a substantial inter- and transdisciplinary semiotic theory which integrates, on the one hand, second-order cybernetics and autopoiesis theory...

  8. Evolutionary Design of Boolean Functions

    Institute of Scientific and Technical Information of China (English)

    WANG Zhang-yi; ZHANG Huan-guo; QIN Zhong-ping; MENG Qing-shu

    2005-01-01

    We use evolutionary computing to synthesize Boolean functions randomly. By using specific crossover and mutation operator in evolving process and modifying search space and fitness function, we get some high non-linearity functions which have other good cryptography characteristics such as autocorrelation etc. Comparing to other heuristic search techniques, evolutionary computing approach is more effective because of global search strategy and implicit parallelism.

  9. Topics of Evolutionary Computation 2001

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem......This booklet contains the student reports from the course: Topics of Evolutionary Computation, Fall 2001, given by Thiemo Krink, Rene Thomsen and Rasmus K. Ursem...

  10. Open Issues in Evolutionary Robotics.

    Science.gov (United States)

    Silva, Fernando; Duarte, Miguel; Correia, Luís; Oliveira, Sancho Moura; Christensen, Anders Lyhne

    2016-01-01

    One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

  11. Evolutionary trends in directional hearing

    DEFF Research Database (Denmark)

    Carr, Catherine E; Christensen-Dalsgaard, Jakob

    2016-01-01

    Tympanic hearing is a true evolutionary novelty that arose in parallel within early tetrapods. We propose that in these tetrapods, selection for sound localization in air acted upon pre-existing directionally sensitive brainstem circuits, similar to those in fishes. Auditory circuits in birds...... interactions between coding strategies and evolutionary history....

  12. Evolutionary Explanations of Eating Disorders

    Directory of Open Access Journals (Sweden)

    Igor Kardum

    2008-12-01

    Full Text Available This article reviews several most important evolutionary mechanisms that underlie eating disorders. The first part clarifies evolutionary foundations of mental disorders and various mechanisms leading to their development. In the second part selective pressures and evolved adaptations causing contemporary epidemic of obesity as well as differences in dietary regimes and life-style between modern humans and their ancestors are described. Concerning eating disorders, a number of current evolutionary explanations of anorexia nervosa are presented together with their main weaknesses. Evolutionary explanations of eating disorders based on the reproductive suppression hypothesis and its variants derived from kin selection theory and the model of parental manipulation were elaborated. The sexual competition hypothesis of eating disorder, adapted to flee famine hypothesis as well as explanation based on the concept of social attention holding power and the need to belonging were also explained. The importance of evolutionary theory in modern conceptualization and research of eating disorders is emphasized.

  13. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  14. Towards an evolutionary theory of language.

    Science.gov (United States)

    Nowak, M A.; Komarova, N L.

    2001-07-01

    Language is a biological trait that radically changed the performance of one species and the appearance of the planet. Understanding how human language came about is one of the most interesting tasks for evolutionary biology. Here we discuss how natural selection can guide the emergence of some basic features of human language, including arbitrary signs, words, syntactic communication and grammar. We show how natural selection can lead to the duality of patterning of human language: sequences of phonemes form words; sequences of words form sentences. Finally, we present a framework for the population dynamics of grammar acquisition, which allows us to study the cultural evolution of grammar and the biological evolution of universal grammar.

  15. Evolutionary paths of streptococcal and staphylococcal superantigens

    Directory of Open Access Journals (Sweden)

    Okumura Kayo

    2012-08-01

    Full Text Available Abstract Background Streptococcus pyogenes (GAS harbors several superantigens (SAgs in the prophage region of its genome, although speG and smez are not located in this region. The diversity of SAgs is thought to arise during horizontal transfer, but their evolutionary pathways have not yet been determined. We recently completed sequencing the entire genome of S. dysgalactiae subsp. equisimilis (SDSE, the closest relative of GAS. Although speG is the only SAg gene of SDSE, speG was present in only 50% of clinical SDSE strains and smez in none. In this study, we analyzed the evolutionary paths of streptococcal and staphylococcal SAgs. Results We compared the sequences of the 12–60 kb speG regions of nine SDSE strains, five speG+ and four speG–. We found that the synteny of this region was highly conserved, whether or not the speG gene was present. Synteny analyses based on genome-wide comparisons of GAS and SDSE indicated that speG is the direct descendant of a common ancestor of streptococcal SAgs, whereas smez was deleted from SDSE after SDSE and GAS split from a common ancestor. Cumulative nucleotide skew analysis of SDSE genomes suggested that speG was located outside segments of steeper slopes than the stable region in the genome, whereas the region flanking smez was unstable, as expected from the results of GAS. We also detected a previously undescribed staphylococcal SAg gene, selW, and a staphylococcal SAg -like gene, ssl, in the core genomes of all Staphylococcus aureus strains sequenced. Amino acid substitution analyses, based on dN/dS window analysis of the products encoded by speG, selW and ssl suggested that all three genes have been subjected to strong positive selection. Evolutionary analysis based on the Bayesian Markov chain Monte Carlo method showed that each clade included at least one direct descendant. Conclusions Our findings reveal a plausible model for the comprehensive evolutionary pathway of streptococcal and

  16. Evolutionary games and quasispecies

    Science.gov (United States)

    Lässig, M.; Tria, F.; Peliti, L.

    2003-05-01

    We discuss a population of sequences subject to mutations and frequency-dependent selection, where the fitness of a sequence depends on the composition of the entire population. This type of dynamics is crucial to understand, for example, the coupled evolution of different strands in a viral population. Mathematically, it takes the form of a reaction-diffusion problem that is nonlinear in the population state. In our model system, the fitness is determined by a simple mathematical game, the hawk-dove game. The stationary population distribution is found to be a quasispecies with properties different from those which hold in fixed fitness landscapes.

  17. The Evolutionary Potential of Phenotypic Mutations.

    Science.gov (United States)

    Yanagida, Hayato; Gispan, Ariel; Kadouri, Noam; Rozen, Shelly; Sharon, Michal; Barkai, Naama; Tawfik, Dan S

    2015-08-01

    Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3'-UTR. Exploring putative cryptic signals in all 3'-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3'-UTR sequences, but also boost the potential for future genetic adaptations.

  18. Evolutionary inference via the Poisson Indel Process.

    Science.gov (United States)

    Bouchard-Côté, Alexandre; Jordan, Michael I

    2013-01-22

    We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.

  19. Evolutionary patterns and processes

    DEFF Research Database (Denmark)

    Leonardi, Michela; Sanz, Pablo Librado; Der Sarkissian, Clio

    2017-01-01

    Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, ...

  20. The evolutionary history of mitochondrial porins

    Directory of Open Access Journals (Sweden)

    Hausner Georg

    2007-02-01

    Full Text Available Abstract Background Mitochondrial porins, or voltage-dependent anion-selective channels (VDAC allow the passage of small molecules across the mitochondrial outer membrane, and are involved in complex interactions regulating organellar and cellular metabolism. Numerous organisms possess multiple porin isoforms, and initial studies indicated an intriguing evolutionary history for these proteins and the genes that encode them. Results In this work, the wealth of recent sequence information was used to perform a comprehensive analysis of the evolutionary history of mitochondrial porins. Fungal porin sequences were well represented, and newly-released sequences from stramenopiles, alveolates, and seed and flowering plants were analyzed. A combination of Neighbour-Joining and Bayesian methods was used to determine phylogenetic relationships among the proteins. The aligned sequences were also used to reassess the validity of previously described eukaryotic porin motifs and to search for signature sequences characteristic of VDACs from plants, animals and fungi. Secondary structure predictions were performed on the aligned VDAC primary sequences and were used to evaluate the sites of intron insertion in a representative set of the corresponding VDAC genes. Conclusion Our phylogenetic analysis clearly shows that paralogs have appeared several times during the evolution of VDACs from the plants, metazoans, and even the fungi, suggesting that there are no "ancient" paralogs within the gene family. Sequence motifs characteristic of the members of the crown groups of organisms were identified. Secondary structure predictions suggest a common 16 β-strand framework for the transmembrane arrangement of all porin isoforms. The GLK (and homologous or analogous motifs and the eukaryotic porin motifs in the four representative Chordates tend to be in exons that appear to have changed little during the evolution of these metazoans. In fact there is phase

  1. Evolutionary financial market models

    Science.gov (United States)

    Ponzi, A.; Aizawa, Y.

    2000-12-01

    We study computer simulations of two financial market models, the second a simplified model of the first. The first is a model of the self-organized formation and breakup of crowds of traders, motivated by the dynamics of competitive evolving systems which shows interesting self-organized critical (SOC)-type behaviour without any fine tuning of control parameters. This SOC-type avalanching and stasis appear as realistic volatility clustering in the price returns time series. The market becomes highly ordered at ‘crashes’ but gradually loses this order through randomization during the intervening stasis periods. The second model is a model of stocks interacting through a competitive evolutionary dynamic in a common stock exchange. This model shows a self-organized ‘market-confidence’. When this is high the market is stable but when it gets low the market may become highly volatile. Volatile bursts rapidly increase the market confidence again. This model shows a phase transition as temperature parameter is varied. The price returns time series in the transition region is very realistic power-law truncated Levy distribution with clustered volatility and volatility superdiffusion. This model also shows generally positive stock cross-correlations as is observed in real markets. This model may shed some light on why such phenomena are observed.

  2. Evolutionary cytogenetics in salamanders.

    Science.gov (United States)

    Sessions, Stanley K

    2008-01-01

    Salamanders (Amphibia: Caudata/Urodela) have been the subject of numerous cytogenetic studies, and data on karyotypes and genome sizes are available for most groups. Salamanders show a more-or-less distinct dichotomy between families with large chromosome numbers and interspecific variation in chromosome number, relative size, and shape (i.e. position of the centromere), and those that exhibit very little variation in these karyological features. This dichotomy is the basis of a major model of karyotype evolution in salamanders involving a kind of 'karyotypic orthoselection'. Salamanders are also characterized by extremely large genomes (in terms of absolute mass of nuclear DNA) and extensive variation in genome size (and overall size of the chromosomes), which transcends variation in chromosome number and shape. The biological significance and evolution of chromosome number and shape within the karyotype is not yet understood, but genome size variation has been found to have strong phenotypic, biogeographic, and phylogenetic correlates that reveal information about the biological significance of this cytogenetic variable. Urodeles also present the advantage of only 10 families and less than 600 species, which facilitates the analysis of patterns within the entire order. The purpose of this review is to present a summary of what is currently known about overall patterns of variation in karyology and genome size in salamanders. These patterns are discussed within an evolutionary context.

  3. The mathematical law of evolutionary information dynamics and an observer's evolution regularities

    CERN Document Server

    Lerner, Vladimir S

    2011-01-01

    An interactive stochastics, evaluated by an entropy functional (EF) of a random field and informational process' path functional (IPF), allows us modeling the evolutionary information processes and revealing regularities of evolution dynamics. Conventional Shannon's information measure evaluates a sequence of the process' static events for each information state and do not reveal hidden dynamic connections between these events. The paper formulates the mathematical forms of the information regularities, based on a minimax variation principle (VP) for IPF, applied to the evolution's both random microprocesses and dynamic macroprocesses. The paper shows that the VP single form of the mathematical law leads to the following evolutionary regularities: -creation of the order from stochastics through the evolutionary macrodynamics, described by a gradient of dynamic potential, evolutionary speed and the evolutionary conditions of a fitness and diversity; -the evolutionary hierarchy with growing information values a...

  4. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

    Indian Academy of Sciences (India)

    Zhao Jun Shao; Eric Rivals; Na Zhao; Sovan Lek; Jianbo Chang; Patrick Berrebi

    2011-08-01

    The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

  5. Industrial Applications of Evolutionary Algorithms

    CERN Document Server

    Sanchez, Ernesto; Tonda, Alberto

    2012-01-01

    This book is intended as a reference both for experienced users of evolutionary algorithms and for researchers that are beginning to approach these fascinating optimization techniques. Experienced users will find interesting details of real-world problems, and advice on solving issues related to fitness computation, modeling and setting appropriate parameters to reach optimal solutions. Beginners will find a thorough introduction to evolutionary computation, and a complete presentation of all evolutionary algorithms exploited to solve different problems. The book could fill the gap between the

  6. Adaptive Evolutionary Analysis of Chloroplast Genes in Euphyllophytes Based on Complete Chloroplast Genome Sequences%基于叶绿体基因组全序列分析真叶植物叶绿体基因的适应性进化

    Institute of Scientific and Technical Information of China (English)

    王博; 高磊; 苏应娟; 王艇

    2012-01-01

    Euphyllophytes comprise fems, gymnosperms, and angiosperms. Relatively abundant chloro-plast genome sequence data has been available for them. In this research, chloroplast gene sequences of 29 euphyllophyte species were extracted from their completely sequenced chloroplast genomes; then an a-daptive evolutionary analysis was performed on the chloroplast genes by running PAML under models allowing w (nonsynonymous/synonymous rate ratio) to vary among sites. The results showed that: ①The percentage of chloroplast genes under positive selection in ferns, gymnosperms, and angiosperms were 6. 5%, 7.5% and 19. 2% , respectively. The number of positively selected genes in angiosperms appeared significantly larger than that of ferns and gymnosperms. ②Most positively selected genes were genetic system or photosynthesis-related genes. Their coding proteins often functioned in chloroplast protein synthesis, gene transcription, energy transformation and regulation, and photosynthesis. We infer that the chloroplast functional genes may have played key roles during the adaptation of euphyllophytes to terrestrial ecosystems.%真叶植物包括蕨类、裸子植物和被子植物.迄今已积累有较为丰富的真叶植物叶绿体基因组全序列数据.选取了29种真叶植物的叶绿体基因组全序列,采用PAML软件基于位点间可变ω模型,分别分析了蕨类、裸子植物和被子植物叶绿体基因的适应性进化.结果显示:①蕨类、裸子植物和被子植物各有6.5%、7.5%和19.2%的叶绿体基因受正选择作用;被子植物经历正选择的叶绿体基因明显比蕨类和裸子植物为多;②被正选择作用的叶绿体基因主要是遗传系统和光合系统基因,它们的编码产物涉及叶绿体蛋白质合成、基因转录、能量转化与调节及光合作用等过程.推测叶绿体功能基因可能在真叶植物对陆生生态环境的适应过程中起着重要作用.

  7. Evolutionary computation for reinforcement learning

    NARCIS (Netherlands)

    S. Whiteson

    2012-01-01

    Algorithms for evolutionary computation, which simulate the process of natural selection to solve optimization problems, are an effective tool for discovering high-performing reinforcement-learning policies. Because they can automatically find good representations, handle continuous action spaces, a

  8. Evolutionary disarmament in interspecific competition.

    Science.gov (United States)

    Kisdi, E; Geritz, S A

    2001-12-22

    Competitive asymmetry, which is the advantage of having a larger body or stronger weaponry than a contestant, drives spectacular evolutionary arms races in intraspecific competition. Similar asymmetries are well documented in interspecific competition, yet they seldom lead to exaggerated traits. Here we demonstrate that two species with substantially different size may undergo parallel coevolution towards a smaller size under the same ecological conditions where a single species would exhibit an evolutionary arms race. We show that disarmament occurs for a wide range of parameters in an ecologically explicit model of competition for a single shared resource; disarmament also occurs in a simple Lotka-Volterra competition model. A key property of both models is the interplay between evolutionary dynamics and population density. The mechanism does not rely on very specific features of the model. Thus, evolutionary disarmament may be widespread and may help to explain the lack of interspecific arms races.

  9. Evolutionary constraints or opportunities?

    Science.gov (United States)

    Sharov, Alexei A.

    2014-01-01

    Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term “constraint” has negative connotations, I use the term “regulated variation” to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch “on” or “off” preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). PMID:24769155

  10. Optimal Control of Evolutionary Dynamics

    CERN Document Server

    Chakrabarti, Raj; McLendon, George

    2008-01-01

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  11. Schizophrenia-an evolutionary enigma?

    Science.gov (United States)

    Brüne, Martin

    2004-03-01

    The term 'schizophrenia' refers to a group of disorders that have been described in every human culture. Two apparently well established findings have corroborated the need for an evolutionary explanation of these disorders: (1) cross-culturally stable incidence rates and (2) decreased fecundity of the affected individuals. The rationale behind this relates to the evolutionary paradox that susceptibility genes for schizophrenia are obviously preserved in the human genepool, despite fundamental reproductive disadvantages associated with the disorders. Some researchers have therefore proposed that a compensatory advantage must exist in people who are carriers of these genes or in their first-degree relatives. Such advantages were hypothesised to be outside the brain (e.g. greater resistance against toxins or infectious diseases), or within the social domain (e.g. schizotypal shamans, creativity). More specifically, T.J. Crow has suggested an evolutionary theory of schizophrenia that relates the disorders to an extreme of variation of hemispheric specialisation and the evolution of language due to a single gene mutation located on homologous regions of the sex chromosomes. None of the evolutionary scenarios does, however, fully account for the diversity of the symptomatology, nor does any one hypothesis acknowledge the objection that the mere prevalence of a disorder must not be confused with adaptation. In the present article, I therefore discuss the evolutionary hypotheses of schizophrenia, arguing that a symptom-based approach to psychotic disorders in evolutionary perspective may improve upon the existing models of schizophrenia.

  12. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B; Andersen, E S; Damgaard, Christian Kroun

    2004-01-01

    of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem......Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...

  13. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Science.gov (United States)

    Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

    2009-01-01

    Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials

  14. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2009-07-01

    Full Text Available Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB, are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN, euchromatic regions (EU, and an evolutionary breakpoint (EB that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s and endogenous retroviruses (ERVs and a depletion of short interspersed nucleotide elements (SINEs shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33, known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the

  15. Occult hepatitis B infection: an evolutionary scenario

    Directory of Open Access Journals (Sweden)

    Lukashov Vladimir V

    2008-12-01

    Full Text Available Abstract Background Occult or latent hepatitis B virus (HBV infection is defined as infection with detectable HBV DNA and undetectable surface antigen (HBsAg in patients' blood. The cause of an overt HBV infection becoming an occult one is unknown. To gain insight into the mechanism of the development of occult infection, we compared the full-length HBV genome from a blood donor carrying an occult infection (d4 with global genotype D genomes. Results The phylogenetic analysis of polymerase, core and X protein sequences did not distinguish d4 from other genotype D strains. Yet, d4 surface protein formed the evolutionary outgroup relative to all other genotype D strains. Its evolutionary branch was the only one where accumulation of substitutions suggests positive selection (dN/dS = 1.3787. Many of these substitutiions accumulated specifically in regions encoding the core/surface protein interface, as revealed in a 3D-modeled protein complex. We identified a novel RNA splicing event (deleting nucleotides 2986-202 that abolishes surface protein gene expression without affecting polymerase, core and X-protein related functions. Genotype D strains differ in their ability to perform this 2986-202 splicing. Strains prone to 2986-202 splicing constitute a separate clade in a phylogenetic tree of genotype D HBVs. A single substitution (G173T that is associated with clade membership alters the local RNA secondary structure and is proposed to affect splicing efficiency at the 202 acceptor site. Conclusion We propose an evolutionary scenario for occult HBV infection, in which 2986-202 splicing generates intracellular virus particles devoid of surface protein, which subsequently accumulates mutations due to relaxation of coding constraints. Such viruses are deficient of autonomous propagation and cannot leave the host cell until it is lysed.

  16. Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes.

    Science.gov (United States)

    Kohli, Gurjeet S; John, Uwe; Van Dolah, Frances M; Murray, Shauna A

    2016-08-01

    Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success.

  17. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Science.gov (United States)

    Blackstone, Neil W.

    2016-01-01

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

  18. An Evolutionary Framework for Understanding the Origin of Eukaryotes.

    Science.gov (United States)

    Blackstone, Neil W

    2016-04-27

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  19. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Directory of Open Access Journals (Sweden)

    Neil W. Blackstone

    2016-04-01

    Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  20. Development of a maize molecular evolutionary genomic database.

    Science.gov (United States)

    Du, Chunguang; Buckler, Edward; Muse, Spencer

    2003-01-01

    PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on 'Maize Evolutionary Genomics'. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence data submission tool has been created that allows project researchers to remotely submit their DNA sequence data directly to PANZEA. On-line database search forms and reports have been created to allow users to search or download germplasm, DNA sequence, gene/locus data and much more, directly from the web.

  1. Structural symmetry in evolutionary games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-10-06

    In evolutionary game theory, an important measure of a mutant trait (strategy) is its ability to invade and take over an otherwise-monomorphic population. Typically, one quantifies the success of a mutant strategy via the probability that a randomly occurring mutant will fixate in the population. However, in a structured population, this fixation probability may depend on where the mutant arises. Moreover, the fixation probability is just one quantity by which one can measure the success of a mutant; fixation time, for instance, is another. We define a notion of homogeneity for evolutionary games that captures what it means for two single-mutant states, i.e. two configurations of a single mutant in an otherwise-monomorphic population, to be 'evolutionarily equivalent' in the sense that all measures of evolutionary success are the same for both configurations. Using asymmetric games, we argue that the term 'homogeneous' should apply to the evolutionary process as a whole rather than to just the population structure. For evolutionary matrix games in graph-structured populations, we give precise conditions under which the resulting process is homogeneous. Finally, we show that asymmetric matrix games can be reduced to symmetric games if the population structure possesses a sufficient degree of symmetry.

  2. The major synthetic evolutionary transitions

    Science.gov (United States)

    Solé, Ricard

    2016-01-01

    Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431528

  3. Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events.

    Science.gov (United States)

    Wang, Xiyin; Wang, Jingpeng; Jin, Dianchuan; Guo, Hui; Lee, Tae-Ho; Liu, Tao; Paterson, Andrew H

    2015-06-01

    Multiple comparisons among genomes can clarify their evolution, speciation, and functional innovations. To date, the genome sequences of eight grasses representing the most economically important Poaceae (grass) clades have been published, and their genomic-level comparison is an essential foundation for evolutionary, functional, and translational research. Using a formal and conservative approach, we aligned these genomes. Direct comparison of paralogous gene pairs all duplicated simultaneously reveal striking variation in evolutionary rates among whole genomes, with nucleotide substitution slowest in rice and up to 48% faster in other grasses, adding a new dimension to the value of rice as a grass model. We reconstructed ancestral genome contents for major evolutionary nodes, potentially contributing to understanding the divergence and speciation of grasses. Recent fossil evidence suggests revisions of the estimated dates of key evolutionary events, implying that the pan-grass polyploidization occurred ∼96 million years ago and could not be related to the Cretaceous-Tertiary mass extinction as previously inferred. Adjusted dating to reflect both updated fossil evidence and lineage-specific evolutionary rates suggested that maize subgenome divergence and maize-sorghum divergence were virtually simultaneous, a coincidence that would be explained if polyploidization directly contributed to speciation. This work lays a solid foundation for Poaceae translational genomics. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

  4. Evolutionary and structural diversity of fungal laccases.

    Science.gov (United States)

    Valderrama, Brenda; Oliver, Patricia; Medrano-Soto, Arturo; Vazquez-Duhalt, Rafael

    2003-01-01

    Fungal laccases have been extensively exploited for industrial purposes and there is a wealth of information available regarding their reaction mechanism, biological role and several molecular aspects, including cloning, heterologous expression and transcriptional analyses. Here we present the reconstruction of the fungal laccase loci evolution inferred from the comparative analysis of 48 different sequences. The topology of the phylogenetic trees indicate that a single monophyletic branch exists for fungal laccases and that laccase isozyme genes may have evolved independently, possibly through duplication-divergence events. Laccases are copper-containing enzymes generally identified by the utilization of substituted p-diphenol substrates. Interestingly, our approach permitted the assignment of two copper-containing oxidases, preliminarily catalogued as laccases, to a different evolutionary group, distantly related to the main branch of bona fide laccases.

  5. Estimating stellar parameters and interstellar extinction from evolutionary tracks

    Science.gov (United States)

    Sichevsky, S.; Malkov, O.

    Developing methods for analyzing and extracting information from modern sky surveys is a challenging task in astrophysical studies. We study possibilities of parameterizing stars and interstellar medium from multicolor photometry performed in three modern photometric surveys: GALEX, SDSS, and 2MASS. For this purpose, we have developed a method to estimate stellar radius from effective temperature and gravity with the help of evolutionary tracks and model stellar atmospheres. In accordance with the evolution rate at every point of the evolutionary track, star formation rate, and initial mass function, a weight is assigned to the resulting value of radius that allows us to estimate the radius more accurately. The method is verified for the most populated areas of the Hertzsprung-Russell diagram: main-sequence stars and red giants, and it was found to be rather precise (for main-sequence stars, the average relative error of radius and its standard deviation are 0.03% and 3.87%, respectively).

  6. Identification and Evolutionary Characterization of ARGONAUTE-Binding Platforms.

    Science.gov (United States)

    Trujillo, Joshua T; Mosher, Rebecca A

    2017-01-01

    ARGONAUTE (AGO) proteins are eukaryotic RNA silencing effectors that interact with their binding partners via short peptide motifs known as AGO hooks. AGO hooks tend to cluster in one region of the protein to create an AGO-binding platform. In addition to the presence of AGO hooks, AGO-binding platforms are intrinsically disordered, contain tandem repeat arrays, and have weak sequence conservation even between close relatives. These characteristics make it difficult to identify and perform evolutionary analysis of these regions. Because of their weak sequence conservation, only a few AGO-binding platforms are characterized, and the evolution of these regions is only poorly understood. In this chapter we describe modules developed for computational identification and evolutionary analysis of AGO-binding platforms, with particular emphasis on understanding evolution of the tandem repeat arrays.

  7. Neuronal boost to evolutionary dynamics.

    Science.gov (United States)

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-06

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

  8. Neuronal boost to evolutionary dynamics

    Science.gov (United States)

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  9. Multivariate Evolutionary Analyses in Astrophysics

    CERN Document Server

    Fraix-Burnet, Didier

    2011-01-01

    The large amount of data on galaxies, up to higher and higher redshifts, asks for sophisticated statistical approaches to build adequate classifications. Multivariate cluster analyses, that compare objects for their global similarities, are still confidential in astrophysics, probably because their results are somewhat difficult to interpret. We believe that the missing key is the unavoidable characteristics in our Universe: evolution. Our approach, known as Astrocladistics, is based on the evolutionary nature of both galaxies and their properties. It gathers objects according to their "histories" and establishes an evolutionary scenario among groups of objects. In this presentation, I show two recent results on globular clusters and earlytype galaxies to illustrate how the evolutionary concepts of Astrocladistics can also be useful for multivariate analyses such as K-means Cluster Analysis.

  10. Evolutionary engineering for industrial microbiology.

    Science.gov (United States)

    Vanee, Niti; Fisher, Adam B; Fong, Stephen S

    2012-01-01

    Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

  11. Molecular Evolutionary Relationships of Enteroinvasive Escherichia coli and Shigella spp.

    OpenAIRE

    Lan, Ruiting; Alles, M. Chehani; Donohoe, Kathy; Marina B Martinez; Reeves, Peter R.

    2004-01-01

    Enteroinvasive Escherichia coli (EIEC), a distinctive pathogenic form of E. coli causing dysentery, is similar in many properties to bacteria placed in the four species of Shigella. Shigella has been separated as a genus but in fact comprises several clones of E. coli. The evolutionary relationships of 32 EIEC strains of 12 serotypes have been determined by sequencing of four housekeeping genes and two plasmid genes which were used previously to determine the relationships of Shigella strains...

  12. Using Ancient DNA to Understand Evolutionary and Ecological Processes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Cooper, Alan

    2014-01-01

    Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies...... modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships...

  13. Generalized topological spaces in evolutionary theory and combinatorial chemistry.

    Science.gov (United States)

    Stadler, Bärbel M R; Stadler, Peter F

    2002-01-01

    The search spaces in combinatorial chemistry as well as the sequence spaces underlying (molecular) evolution are conventionally thought of as graphs. Recombination, however, implies a nongraphical structure of the combinatorial search spaces. These structures, and their implications for search process itself, are heretofore not well understood in general. In this contribution we review a very general formalism from point set topology and discuss its application to combinatorial search spaces, fitness landscapes, evolutionary trajectories, and artificial chemistries.

  14. Evolutionary optimization of optical antennas

    CERN Document Server

    Feichtner, Thorsten; Kiunke, Markus; Hecht, Bert

    2012-01-01

    The design of nano-antennas is so far mainly inspired by radio-frequency technology. However, material properties and experimental settings need to be reconsidered at optical frequencies, which entails the need for alternative optimal antenna designs. Here a checkerboard-type, initially random array of gold cubes is subjected to evolutionary optimization. To illustrate the power of the approach we demonstrate that by optimizing the near-field intensity enhancement the evolutionary algorithm finds a new antenna geometry, essentially a split-ring/two-wire antenna hybrid which surpasses by far the performance of a conventional gap antenna by shifting the n=1 split-ring resonance into the optical regime.

  15. Evolutionary Aesthetics and Print Advertising

    Directory of Open Access Journals (Sweden)

    Kamil Luczaj

    2015-06-01

    Full Text Available The article analyzes the extent to which predictions based on the theory of evolutionary aesthetics are utilized by the advertising industry. The purpose of a comprehensive content analysis of print advertising is to determine whether the items indicated by evolutionists such as animals, flowers, certain types of landscapes, beautiful humans, and some colors are part of real advertising strategies. This article has shown that many evolutionary hypotheses (although not all of them are supported by empirical data. Along with these hypotheses, some inferences from Bourdieu’s cultural capital theory were tested. It turned out that advertising uses both biological schemata and cultural patterns to make an image more likable.

  16. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  17. Diversity-Guided Evolutionary Algorithms

    DEFF Research Database (Denmark)

    Ursem, Rasmus Kjær

    2002-01-01

    Population diversity is undoubtably a key issue in the performance of evolutionary algorithms. A common hypothesis is that high diversity is important to avoid premature convergence and to escape local optima. Various diversity measures have been used to analyze algorithms, but so far few...... algorithms have used a measure to guide the search. The diversity-guided evolutionary algorithm (DGEA) uses the wellknown distance-to-average-point measure to alternate between phases of exploration (mutation) and phases of exploitation (recombination and selection). The DGEA showed remarkable results...

  18. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  19. Evolutionary process of deep-sea bathymodiolus mussels.

    Directory of Open Access Journals (Sweden)

    Jun-Ichi Miyazaki

    Full Text Available BACKGROUND: Since the discovery of deep-sea chemosynthesis-based communities, much work has been done to clarify their organismal and environmental aspects. However, major topics remain to be resolved, including when and how organisms invade and adapt to deep-sea environments; whether strategies for invasion and adaptation are shared by different taxa or unique to each taxon; how organisms extend their distribution and diversity; and how they become isolated to speciate in continuous waters. Deep-sea mussels are one of the dominant organisms in chemosynthesis-based communities, thus investigations of their origin and evolution contribute to resolving questions about life in those communities. METHODOLOGY/PRINCIPAL FINDING: We investigated worldwide phylogenetic relationships of deep-sea Bathymodiolus mussels and their mytilid relatives by analyzing nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI and NADH dehydrogenase subunit 4 (ND4 genes. Phylogenetic analysis of the concatenated sequence data showed that mussels of the subfamily Bathymodiolinae from vents and seeps were divided into four groups, and that mussels of the subfamily Modiolinae from sunken wood and whale carcasses assumed the outgroup position and shallow-water modioline mussels were positioned more distantly to the bathymodioline mussels. We provisionally hypothesized the evolutionary history of Bathymodilolus mussels by estimating evolutionary time under a relaxed molecular clock model. Diversification of bathymodioline mussels was initiated in the early Miocene, and subsequently diversification of the groups occurred in the early to middle Miocene. CONCLUSIONS/SIGNIFICANCE: The phylogenetic relationships support the "Evolutionary stepping stone hypothesis," in which mytilid ancestors exploited sunken wood and whale carcasses in their progressive adaptation to deep-sea environments. This hypothesis is also supported by the evolutionary transition of

  20. The evolutionary history of Cys-tRNACys formation.

    Science.gov (United States)

    O'Donoghue, Patrick; Sethi, Anurag; Woese, Carl R; Luthey-Schulten, Zaida A

    2005-12-27

    The recent discovery of an alternate pathway for indirectly charging tRNA(Cys) has stimulated a re-examination of the evolutionary history of Cys-tRNA(Cys) formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA(Cys) with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA(Cys) aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.

  1. Evolutionary perspective in child growth.

    Science.gov (United States)

    Hochberg, Ze'ev

    2011-07-01

    Hereditary, environmental, and stochastic factors determine a child's growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment.

  2. Evolutionary Perspective in Child Growth

    Directory of Open Access Journals (Sweden)

    Ze’ev Hochberg

    2011-07-01

    Full Text Available Hereditary, environmental, and stochastic factors determine a child’s growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment.

  3. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    enetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  4. Current Issues in Evolutionary Paleontology.

    Science.gov (United States)

    Scully, Erik Paul

    1987-01-01

    Describes some of the contributions made by the field of paleontology to theories in geology and biology. Suggests that the two best examples of modern evolutionary paleontology relate to the theory of punctuated equilibria, and the possibility that mass extinctions may be cyclic. (TW)

  5. Evolutionary Computation and its Application

    Institute of Scientific and Technical Information of China (English)

    Licheng Jiao; Lishan Kang; Zhenya He; Tao Xie

    2006-01-01

    @@ On Mar.23,2006,a project in the Major Program of NSFC-"Evolutionary computation and its application",managed by Prof.Licheng Jiao,Prof.Lishan Kang,Prof.Zhenya He,and Prof.Tao Xie,passed its Final Qualification Process and was evaluated as Excellent.

  6. Evolutionary models of human personality

    NARCIS (Netherlands)

    Haysom, H.J.; Verweij, C.J.H.; Zietsch, B.P.

    2015-01-01

    Behavioral genetic studies have shown that around a third to a half of the between-individual variation in personality traits can be accounted for by genetic differences between individuals. There is rapidly growing interest in understanding the evolutionary basis of this genetic variation. In this

  7. Is evolutionary biology strategic science?

    Science.gov (United States)

    Meagher, Thomas R

    2007-01-01

    There is a profound need for the scientific community to be better aware of the policy context in which it operates. To address this need, Evolution has established a new Outlook feature section to include papers that explore the interface between society and evolutionary biology. This first paper in the series considers the strategic relevance of evolutionary biology. Support for scientific research in general is based on governmental or institutional expenditure that is an investment, and such investment is based on strategies designed to achieve particular outcomes, such as advance in particular areas of basic science or application. The scientific community can engage in the development of scientific strategies on a variety of levels, including workshops to explicitly develop research priorities and targeted funding initiatives to help define emerging scientific areas. Better understanding and communication of the scientific achievements of evolutionary biology, emphasizing immediate and potential societal relevance, are effective counters to challenges presented by the creationist agenda. Future papers in the Outlook feature section should assist the evolutionary biology community in achieving a better collective understanding of the societal relevance of their field.

  8. Scalable Computing for Evolutionary Genomics

    NARCIS (Netherlands)

    Prins, J.C.P.; Belhachemi, D.; Möller, S.; Smant, G.

    2012-01-01

    Genomic data analysis in evolutionary biology is becoming so computationally intensive that analysis of multiple hypotheses and scenarios takes too long on a single desktop computer. In this chapter, we discuss techniques for scaling computations through parallelization of calculations, after giving

  9. Functional morphology and evolutionary biology.

    Science.gov (United States)

    Dullemeijer, P

    1980-01-01

    In this study the relationship between functional morpholoy and evolutionary biology is analysed by confronting the main concepts in both disciplines. Rather than only discussing this connection theoretically, the analysis is carried out by introducing important practical and experimental studies, which use aspects from both disciplines. The mentioned investigations are methodologically analysed and the consequences for extensions of the relationship are worked out. It can be shown that both disciplines have a large domain of their own and also share a large common ground. Many disagreements among evolutionary biologists can be reduced to differences in general philosophy (idealism vs. realism), selection of phenomenona (structure vs. function), definition of concepts (natural selection) and the position of the concept theory as an explaining factor (neutralists vs selectionist, random variation, determinate selection, etc.). The significance of functional morphology for evolutionary biology, and vice versa depends on these differences. For a neo-Darwinian evolutionary theory, contributions from functional and ecological morphology are indispensable. Of ultimate importance are the notions of internal selection and constraints in the constructions determining further development. In this context the concepts of random variation and natural selection need more detailed definition. The study ends with a recommendation for future research founded in a system-theoretical or structuralistic conception.

  10. Statistical Methods for Evolutionary Trees

    OpenAIRE

    Edwards, A. W. F.

    2009-01-01

    In 1963 and 1964, L. L. Cavalli-Sforza and A. W. F. Edwards introduced novel methods for computing evolutionary trees from genetical data, initially for human populations from blood-group gene frequencies. The most important development was their introduction of statistical methods of estimation applied to stochastic models of evolution.

  11. Micro Evolutionary Processes and Adaptation

    Institute of Scientific and Technical Information of China (English)

    SHADMANOV; R; K; RUBAN; I; N; VOROPAEVA; N; L; SHADMANOVA; A; R

    2008-01-01

    It would be well to note that in the absence of clear data about the formation of adaptation systems,or mechanisms of their occurrence,all that is recognized is the realization of the micro evolutionary processes.There is no well-defined connection between information exchange and formation of

  12. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  13. Realism, Relativism, and Evolutionary Psychology

    NARCIS (Netherlands)

    Derksen, M.

    Against recent attempts to forge a reconciliation between constructionism and realism, I contend that, in psychology at least, stirring up conflict is a more fruitful strategy. To illustrate this thesis, I confront a school of psychology with strong realist leanings, evolutionary psychology, with

  14. Evolutionary Psychology and Intelligence Research

    Science.gov (United States)

    Kanazawa, Satoshi

    2010-01-01

    This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…

  15. Statistical methods for evolutionary trees.

    Science.gov (United States)

    Edwards, A W F

    2009-09-01

    In 1963 and 1964, L. L. Cavalli-Sforza and A. W. F. Edwards introduced novel methods for computing evolutionary trees from genetical data, initially for human populations from blood-group gene frequencies. The most important development was their introduction of statistical methods of estimation applied to stochastic models of evolution.

  16. Evolutionary rate patterns of the Gibberellin pathway genes

    Directory of Open Access Journals (Sweden)

    Zhang Fu-min

    2009-08-01

    Full Text Available Abstract Background Analysis of molecular evolutionary patterns of different genes within metabolic pathways allows us to determine whether these genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution of proteins in an interacting system. Although previous studies found that upstream genes in the pathway evolved more slowly than downstream genes, the correlation between evolutionary rate and position of the genes in metabolic pathways as well as its implications in molecular evolution are still less understood. Results We sequenced and characterized 7 core structural genes of the gibberellin biosynthetic pathway from 8 representative species of the rice tribe (Oryzeae to address alternative hypotheses regarding evolutionary rates and patterns of metabolic pathway genes. We have detected significant rate heterogeneity among 7 GA pathway genes for both synonymous and nonsynonymous sites. Such rate variation is mostly likely attributed to differences of selection intensity rather than differential mutation pressures on the genes. Unlike previous argument that downstream genes in metabolic pathways would evolve more slowly than upstream genes, the downstream genes in the GA pathway did not exhibited the elevated substitution rate and instead, the genes that encode either the enzyme at the branch point (GA20ox or enzymes catalyzing multiple steps (KO, KAO and GA3ox in the pathway had the lowest evolutionary rates due to strong purifying selection. Our branch and codon models failed to detect signature of positive selection for any lineage and codon of the GA pathway genes. Conclusion This study suggests that significant heterogeneity of evolutionary rate of the GA pathway genes is mainly ascribed to differential constraint relaxation rather than the positive selection and supports the pathway flux theory that predicts that natural selection primarily targets enzymes that have the greatest control on fluxes.

  17. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  18. MULTI-WORLD MECHANISM FOR MODELING EVOLUTIONARY DESIGN PROCESS FROM CONCEPTUAL DESIGN TO DETAILED DESIGN

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A multi-world mechanism is developed for modeling evolutionary design process from conceptual design to detailed design. In this mechanism, the evolutionary design database is represented by a sequence of worlds corresponding to the design descriptions at different design stages. In each world, only the differences with its ancestor world are recorded. When the design descriptions in one world are changed, these changes are then propagated to its descendant worlds automatically. Case study is conducted to show the effectiveness of this evolutionary design database model.

  19. Remarkable evolutionary conservation of SOX14 orthologues

    Indian Academy of Sciences (India)

    Jelena Popovic; Milena Stevanovic

    2009-04-01

    SOX proteins constitute a large family of diverse, well-conserved transcription factors present in vertebrates and invertebrates, and also implicated in control of many developmental processes. Our objectives have been to identify Sox14 gene of goat (Capra hircus), cow (Bos taurus) and rat (Rattus norvegicus), and to perform comparative analyses and mapping of SOX14 orthologues from numerous vertebrate species. PCR based approach was used to identify Sox14 of goat, cow and rat, while nucleotide and amino acid sequence alignments and mapping were performed using information currently available in public database. Comparative sequence analysis revealed remarkable identity among Sox14 orthologues and helped us to identify highly conserved motifs that represent molecular signatures of SOX14 protein that might have structural or functional significance. Further, we determined chromosomal locations of numerous predicted group B Sox genes and their neighbouring genes using currently available genome database. In conclusion, our study has not only supported the proposed model of group B Sox genes evolution in chicken and mammals, but has also revealed that additional evolutionary events split Sox B genes into different chromosomes in some mammals. Mapping data presented in this study could help in refining the understanding of the evolution of group B Sox genes in vertebrates.

  20. Evolutionary dynamics of Newcastle disease virus

    Science.gov (United States)

    Miller, P.J.; Kim, L.M.; Ip, H.S.; Afonso, C.L.

    2009-01-01

    A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an increase in virulence may accelerate the rate of NDV evolution. ?? 2009 Elsevier Inc.