arXiv subjects

C. Pinto

Publications and source records attributed to C. Pinto.

At least 145 records · Page 8Linked to original sources

arXiv2014

Multiwavelength campaign on Mrk 509. XIII. Testing ionized-reflection models on Mrk 509

Active Galactic Nuclei (AGN) are the most luminous persistent objects in the universe. An excess of X-ray emission below about 2 keV, called soft-excess, is very common in Type 1 AGN spectra. The origin of this feature remains debated. Originally modeled with a blackbody, there are now several possibilities to model the soft-excess, including warm Comptonization and blurred ionized reflection. In this paper, we test ionized-reflection models on Mrk 509, a bright Seyfert 1 galaxy for which we have a unique data set, in order to determine whether it can be responsible for the strong soft-excess. We use ten simultaneous XMM-Newton and INTEGRAL observations performed every four days. We present here the results of the spectral analysis, the evolution of the parameters and the variability properties of the X-ray emission. The application of blurred ionized-reflection models leads to a very strong reflection and an extreme geometry, but fails to reproduce the broad-band spectrum of Mrk 509. Two different scenarios for blurred ionized reflection are discussed: stable geometry and lamp-post configuration. In both cases we find that the model parameters do not follow the expected relations, indicating that the model is fine-tuned to fit the data without physical justification. A large, slow variation of the soft-excess without counterpart in the hard X-rays could be explained by a change in ionization of the reflector. However, such a change does not naturally follow from the assumed geometrical configuration. Warm Comptonization remains the most probable origin of the soft-excess in this object. Nevertheless, it is possible that both ionized reflection and warm Comptonization mechanisms can explain the soft-excess in all objects, one dominating the other one, depending on the physical conditions of the disk and the corona.

astro-ph.HE↗

arXiv2013

The Hot and Energetic Universe: The astrophysics of supernova remnants and the interstellar medium

The study of both supernova remnants and the hot and cold phases of the interstellar medium are essential for understanding the final stages of stellar evolution and their feedback on the evolution of galaxies through injection of energy and heavy elements. These studies are also crucial for understanding the physics of supernovae, their cosmological implication, and the origin of galactic cosmic rays. The unique capabilities of Athena+ will allow us to explore a new parameter space. Spatially-resolved high-resolution spectroscopy using Athena+ X-IFU of young remnants will allow to characterize individual parcels of ejected material in the line of sight in terms of kinematics, ionization and composition, providing access to the three dimensional geometry of the explosion. Athena+ will also allow studying shock physics and particle acceleration in supernova remnants, as well as their interaction with their environment. Athena+ X-IFU will also characterize the ionization mechanisms competing in forming the complex structures of the hot interstellar medium, likely to keep the echo of past star formation activity, both in our Galaxy and nearby ones. For the first time the dust and gas of the densest cold medium, like in the Galactic Centre environment, will be studied. Athena+ X-IFU will observe, along with the Mg K and Si K edges, which are the main tracers of the silicates content of the ISM, the Fe K edge with unprecedented sensitivity and energy-resolution. This will allow us to study for the first time the nature of Fe-bearing dust in such regions.

astro-ph.HE↗

arXiv2013

Measuring X-ray variability in faint/sparsely-sampled AGN

We study the statistical properties of the Normalized Excess Variance of variability process characterized by a red-noise power spectral density (PSD), as the case of Active Galactic Nuclei (AGN). We perform Monte Carlo simulations of lightcurves, assuming both a continuous and a sparse sampling pattern and various signal-to-noise (S/N) ratios. We show that the normalized excess variance is a biased estimate of the variance even in the case of continuously sampled lightcurves. The bias depends on the PSD slope and on the sampling pattern, but not on the S/N ratio. We provide a simple formula to account for the bias, which yields unbiased estimates with an accuracy better than 15%. We show that the normalized excess variance estimates based on single lightcurves (especially for sparse sampling and S/N less than 3) are highly uncertain (even if corrected for bias) and we propose instead the use of an ensemble estimate, based on multiple lightcurves of the same object, or on the use of lightcurves of many objects. These estimates have symmetric distributions, known errors, and can also be corrected for biases.We use our results to estimate the ability to measure the intrinsic source variability in current data, and show that they could also be useful in the planning of the observing strategy of future surveys such as those provided by X-ray missions studying distant and/or faint AGN populations and, more in general, in the estimation of the variability amplitude of sources that will result from future surveys such as Pan-STARRS, and LSST.

astro-ph.HE↗

arXiv2013

ISM composition through X-ray spectroscopy of LMXBs

The diffuse interstellar medium (ISM) is an integral part of the evolution of the entire Galaxy. Metals are produced by stars and their abundances are the direct testimony of the history of stellar evolution. However, the interstellar dust composition is not well known and the total abundances are yet to be accurately determined. We probe ISM dust composition, total abundances, and abundance gradients through the study of interstellar absorption features in the high-resolution X-ray spectra of Galactic low-mass X-ray binaries (LMXBs). We use high-quality grating spectra of nine LMXBs taken with XMM-Newton. We measure the column densities of O, Ne, Mg, and Fe with an empirical model and estimate the Galactic abundance gradients. The column densities of the neutral gas species are in agreement with those found in the literature. Solids are a significant reservoir of metals like oxygen and iron. Respectively, 15-25 % and 65-90 % of the total amount of O I and Fe I is found in dust. The dust amount and mixture seem to be consistent along all the lines-of-sight (LOS). Our estimates of abundance gradients and predictions of local interstellar abundances are in agreement with those measured at longer wavelengths. Our work shows that X-ray spectroscopy is a very powerful method to probe the ISM. For instance, on a large scale the ISM appears to be chemically homogeneous showing similar gas ionization ratios and dust mixtures. The agreement between the abundances of the ISM and the stellar objects suggests that the local Galaxy is also chemically homogeneous.

astro-ph.GA↗

arXiv2012

Reflection and dissipation of Alfvén waves in interstellar clouds

Context: Supersonic nonthermal motions in molecular clouds are often interpreted as long-lived magnetohydrodynamic (MHD) waves. The propagation and amplitude of these waves is affected by local physical characteristics, most importantly the gas density and the ionization fraction. Aims: We study the propagation, reflection and dissipation of Alfvén waves in molecular clouds deriving the behavior of observable quantities such as the amplitudes of velocity fluctuations and the rate of energy dissipation. Methods: We formulated the problem in terms of Elsässer variables for transverse MHD waves propagating in a one-dimensional inhomogeneous medium, including the dissipation due to collisions between ions and neutrals and to a nonlinear turbulent cascade treated in a phenomenological way. We considered both steady-state and time-dependent situations and solved the equations of the problem numerically with an iterative method and a Lax-Wendroff scheme, respectively. Results: Alfvén waves incident on overdense regions with density profiles typical of cloud cores embedded in a diffuse gas suffer enhanced reflection in the regions of the steepest density gradient, and strong dissipation in the core's interior. These effects are especially significant when the wavelength is intermediate between the critical wavelength for propagation and the typical scale of the density gradient. For larger wave amplitudes and/or steeper input spectra, the effects of the perpendicular turbulent cascade result in a stronger energy dissipation in the regions immediately surrounding the dense core. Conclusions: The results may help to interpret the sharp decrease of line width observed in the environments of low-mass cloud cores in several molecular transitions.

astro-ph.GA↗

arXiv2012

Multiwavelength campaign on Mrk 509: Reverberation of the Fe Kalpha line

We report on a detailed study of the Fe K emission/absorption complex in the nearby, bright Seyfert 1 galaxy Mrk 509. The study is part of an extensive XMM-Newton monitoring consisting of 10 pointings (~60 ks each) about once every four days, and includes also a reanalysis of previous XMM-Newton and Chandra observations. Mrk 509 shows a clear (EW=58 eV) neutral Fe Kalpha emission line that can be decomposed into a narrow (sigma=0.027 keV) component (found in the Chandra HETG data) plus a resolved (sigma=0.22 keV) component. We find the first successful measurement of a linear correlation between the intensity of the resolved line component and the 3-10 keV flux variations on time-scales of years down to a few days. The Fe Kalpha reverberates the hard X-ray continuum without any measurable lag, suggesting that the region producing the resolved Fe Kalpha component is located within a few light days-week (r<~10^3 rg) from the Black Hole (BH). The lack of a redshifted wing in the line poses a lower limit of >40 rg for its distance from the BH. The Fe Kalpha could thus be emitted from the inner regions of the BLR, i.e. within the ~80 light days indicated by the Hbeta line measurements. In addition to these two neutral Fe Kalpha components, we confirm the detection of weak (EW~8-20 eV) ionised Fe K emission. This ionised line can be modeled with either a blend of two narrow FeXXV and FeXXVI emission lines or with a single relativistic line produced, in an ionised disc, down to a few rg from the BH. Finally, we observe a weakening/disappearing of the medium and high velocity high ionisation Fe K wind features found in previous XMM-Newton observations. This campaign has made possible the first reverberation measurement of the resolved component of the Fe Kalpha line, from which we can infer a location for the bulk of its emission at a distance of r~40-1000 rg from the BH.

astro-ph.HE↗

arXiv2012

Multiwavelength campaign on Mrk 509 IX. The Galactic foreground

The diffuse gas in and nearby the Milky Way plays an important role in the evolution of the entire Galaxy. It has a complex structure characterized by neutral, weakly and highly ionized gas, dust, and molecules. We probe this gas through the observation of its absorption lines in the high-energy spectra of background sources. We use high-quality spectra of AGN Mrk 509, located at high Galactic latitudes obtained with XMM-Newton, HST and FUSE. We use advanced absorption models consisting of photo- and collisional-ionization. We constrain the column density ratios of the different phases of the interstellar medium (ISM) and measure the abundances of C, N, O, Ne, Mg, Al, Si, S, and Fe. We detect seven discrete interstellar clouds with different velocities. One is a typical low-velocity cloud (LVC) and three belong to the family of the intermediate-velocity clouds (IVCs) found near the Galactic disk. These four clouds show large deviation from Solar abundances in the gas phase, mostly caused by dust depletion. The other three clouds are ionized high-velocity clouds (HVCs) and are located either in the Galactic environment or in the Local Group halo as suggested by the signatures of collisional ionization. The similar abundances and ionization structure of the HVCs suggest a common location and origin: they might belong to the remainder of an extragalactic cloud which was captured by the Galaxy. We have shown that combined UV / X-ray spectroscopy is a powerful tool to investigate the ISM. In common Galactic clouds, like LVCs and IVCs, the ISM shows a complex structure consisting of at least three different temperature phases.

astro-ph.GA↗

arXiv2012

Multiwavelength campaign on Mrk 509 VIII. Location of the X-ray absorber

The bright Seyfert 1 galaxy Mrk 509 was monitored by XMM-Newton and other satellites in 2009 to constrain the location of the outflow. We have studied the response of the photoionised gas to changes in the ionising flux produced by the central regions. We used the 5 discrete ionisation components A-E detected in the time-averaged spectrum taken with the RGS. Using the ratio of fluxed EPIC and RGS spectra, we put tight constraints on the variability of the absorbers. Monitoring with the Swift satellite started 6 weeks before the XMM-Newton observations, allowing to use the ionising flux history and to develop a model for the time-dependent photoionisation. Components A and B are too weak for variability studies, but the distance for component A is known from optical imaging of the [O III] line to be ~3 kpc. During the 5 weeks of the XMM-Newton observations we found no evidence of changes in the 3 X-ray dominant ionisation components C-E, despite a huge soft X-ray intensity increase of 60% in the middle of our campaign. This excludes high-density gas close to the black hole. Instead, using our time-dependent modelling, we find low density and derive firm lower limits to the distance of these components. Component D shows evidence for variability on longer time scales, yielding an upper limit to the distance. For component E we derive an upper limit to the distance based on the argument that the thickness of the absorbing layer must be less than its distance to the black hole. Combining these results, at the 90% confidence level, component C has a distance of >70 pc, component D between 5-33 pc, and component E >5 pc but smaller than 21-400 pc, depending upon modelling details. These results are consistent with the upper limits from the HST/COS observations of our campaign and point to an origin of the dominant, slow (v<1000 km/s) outflow components in the NLR or torus-region of Mrk 509.

astro-ph.CO↗

arXiv2012

Characterizing the UV and X-ray Outflow in Mrk 509

We observed Mrk 509 during the fall of 2009 during a multiwavelength campaign using XMM-Newton, Chandra, HST/COS, SWIFT, and Integral. The 600-ks XMM/RGS spectrum finds two kinematic components and a discrete distribution of ionized absorbers. Our high S/N COS spectrum detects additional complexity in the known UV absorption troughs from a variety of sources in Mrk 509, including the outflow from the active nucleus, the ISM and halo of the host galaxy, and infalling clouds or stripped gas from a merger that are illuminated by the AGN. The UV absorption only partially covers the emission from the AGN nucleus with covering fractions lower than those previously seen with STIS, and are comparable to those seen with FUSE. Given the larger apertures of COS and FUSE compared to STIS, we favor scattered light from an extended region near the AGN as the explanation for the partial covering. As observed in prior X-ray and UV spectra, the UV absorption has velocities comparable to the X-ray absorption, but the bulk of the ultraviolet absorption is in a lower ionization state with lower total column density than the gas responsible for the X-ray absorption. Variability compared to prior UV spectra lets us set limits on the location, density, mass flux, and kinetic energy of the outflowing gas. For component 1 at $-400 \rm km s^{-1}$, the kinetic energy flux of both the UV and the X-ray outflow is insufficient to have a significant impact on further evolution of the host galaxy.

astro-ph.CO↗

arXiv2011

XMM-Newton observation of 4U 1820-30: Broad band spectrum and the contribution of the cold interstellar medium

We present the analysis of the bright X-ray binary 4U 1820-30, based mainly on XMM-Newton-RGS data, but using complementary data from XMM-Epic, Integral, and Chandra-HETG, to investigate different aspects of the source. The broad band continuum is well fitted by a classical combination of black body and Comptonized emission. The continuum shape and the high flux of the source (L/L_Edd\sim0.16) are consistent with a "high state" of the source. We do not find significant evidence of iron emission at energies >=6.4 keV. The soft X-ray spectrum contain a number of absorption features. Here we focus on the cold-mildly ionized gas. The neutral gas column density is N_H\sim1.63x10^21 cm^-2. The detailed study of the oxygen and iron edge reveals that those elements are depleted, defined here as the ratio between dust and the total ISM cold phase, by a factor 0.20\pm0.02 and 0.87\pm0.14, respectively. Using the available dust models, the best fit points to a major contribution of Mg-rich silicates, with metallic iron inclusion. Although we find that a large fraction of Fe is in dust form, the fit shows that Fe-rich silicates are disfavored. The measured Mg:Fe ratio is 2.0\pm0.3. Interestingly, this modeling may point to a well studied dust constituent (GEMS), sometimes proposed as a silicate constituent in our Galaxy. Oxygen and iron are found to be slightly over- and under-abundant, respectively (1.23 and 0.85 times the solar value) along this line of sight. We also report the detection of two absorption lines, tentatively identified as part of an outflow of mildly ionized gas (ξ\sim-0.5) at a velocity of \sim1200 km/s.

astro-ph.GA↗

arXiv2011

Multiwavelength campaign on Mrk 509 VII. Relative abundances of the warm absorber

Context. The study of abundances in the nucleus of active galaxies allows us to investigate the evolution of abundance by comparing local and higher redshift galaxies. However, the methods used so far have substantial drawbacks or rather large uncertainties. Some of the measurements are at odds with the initial mass function derived from the older stellar population of local elliptical galaxies. Aims. We determine accurate and reliable abundances of C, N, Ne, and Fe relative to O from the narrow absorption lines observed in the X-ray spectra of Mrk 509. Methods. We use the stacked 600 ks XMM-Newton RGS and 180 ks Chandra LETGS spectra. Thanks to simultaneous observations with INTEGRAL and the optical monitor on-board XMM-Newton for the RGS observations and HST-COS and Swift for the LETGS observations, we have an individual spectral energy distribution for each dataset. Owing to the excellent quality of the RGS spectrum, the ionisation structure of the absorbing gas is well constrained, allowing for a reliable abundance determination using ions over the whole observed range of ionisation parameters. Results. We find that the relative abundances are consistent with the proto-solar abundance ratios: C/O = 1.19$\pm$0.08, N/O = 0.98$\pm$0.08, Ne/O = 1.11$\pm$0.10, Mg/O = 0.68$\pm$0.16, Si/O = 1.3$\pm$0.6, Ca/O = 0.89$\pm$0.25, and Fe/O = 0.85$\pm$0.06, with the exception of S, which is slightly under-abundant, S/O = 0.57$\pm$0.14. Our results, and their implications, are discussed and compared to the results obtained using other techniques to derive abundances in galaxies.

astro-ph.CO↗

arXiv2011

Multiwavelength campaign on Mrk 509. I. Variability and spectral energy distribution

(Abridged) Active galactic nuclei show a wealth of interesting physical processes, some of which are poorly understood. We want to address a number of open questions, including the location and physics of the outflow from AGN, the nature of the continuum emission, the geometry and physical state of the X-ray broad emission line region, the Fe-K line complex, the metal abundances of the nucleus and finally the interstellar medium of our own Galaxy. We study one of the best targets for these aims, the Seyfert 1 galaxy Mrk 509 with a multiwavelength campaign using five satellites (XMM-Newton, INTEGRAL, Chandra, HST and Swift) and two ground-based facilities (WHT and PAIRITEL). Our observations cover more than five decades in frequency, from 2 um to 200 keV. The combination of high-resolution spectroscopy and time variability allows us to disentangle and study the different components. Our campaign covers 100 days from September to December 2009, and is centred on a simultaneous set of deep XMM-Newton and INTEGRAL observations with regular time intervals, spanning seven weeks. We obtain a continuous light curve in the X-ray and UV band, showing a strong, up to 60% flux increase in the soft X-ray band during the three weeks in the middle of our deepest monitoring campaign, and which is correlated with an enhancement of the UV flux. This allows us to study the time evolution of the continuum and the outflow. By stacking the observations, we have also obtained one of the best X-ray and UV spectra of a Seyfert galaxy ever obtained. In this paper we also study the effects of the spectral energy distribution (SED) that we obtained on the photo-ionisation equilibrium. Thanks to our broad-band coverage, uncertainties on the SED do not strongly affect the determination of this equilibrium.

astro-ph.CO↗

arXiv2011

Multiwavelength campaign on Mrk 509. II. Analysis of high-quality Reflection Grating Spectrometer spectra

We study the bright Seyfert 1 galaxy Mrk~509 with the Reflection Grating Spectrometers (RGS) of XMM-Newton using the RGS multi-pointing mode of XMM-Newton for the first time in order to constrain the properties of the outflow in this object. We want to obtain the most accurate spectral properties from the 600 ks spectrum of Mrk 509 which has excellent statistical quality. We derive an accurate relative calibration for the effective area of the RGS, derive an accurate absolute wavelength calibration, improve the method for adding time-dependent spectra and enhance the efficiency of the spectral fitting by two orders of magnitude. We show the major improvement of the spectral data quality due to the use of the new RGS multi-pointing mode of XMM-Newton. We illustrate the gain in accuracy by showing that with the improved wavelength calibration the two velocity troughs observed in UV spectra are resolved.

astro-ph.CO↗

arXiv2011

Multiwavelength campaign on Mrk 509. III. The 600 ks RGS spectrum: unravelling the inner region of an AGN

We present the results of our 600 ks RGS observation as part of the multiwavelength campaign on Mrk 509. The very high quality of the spectrum allows us to investigate the ionized outflow with an unprecedented accuracy due to the long exposure and the use of the RGS multipointing mode. We detect multiple absorption lines from the interstellar medium and from the ionized absorber in Mrk 509. A number of emission components are also detected, including broad emission lines consistent with an origin in the broad line region, the narrow OVII forbidden emission line and also (narrow) radiative recombination continua. The ionized absorber consists of two velocity components (v = -13 \pm 11 km/s and v = -319 \pm 14 km/s), which both are consistent with earlier results, including UV data. There is another tentative component outflowing at high velocity, -770 \pm 109 km/s, which is only seen in a few highly ionized absorption lines. The outflow shows discrete ionization components, spanning four orders of magnitude in ionization parameter. Due to the excellent statistics of our spectrum, we demonstrate for the first time that the outflow in Mrk 509 in the important range of log xi between 1-3 cannot be described by a smooth, continuous absorption measure distribution, but instead shows two strong, discrete peaks. At the highest and lowest ionization parameters we cannot differentiate smooth and discrete components.

astro-ph.CO↗

arXiv2011

Multiwavelength campaign on Mrk 509. V. Chandra-LETGS observation of the ionized absorber

We present here the results of a 180 ks Chandra-LETGS observation as part of a large multi-wavelength campaign on Mrk 509. We study the warm absorber in Mrk 509 and use the data from a simultaneous HST-COS observation in order to assess whether the gas responsible for the UV and X-ray absorption are the same. We analyzed the LETGS X-ray spectrum of Mrk 509 using the SPEX fitting package. We detect several absorption features originating in the ionized absorber of the source, along with resolved emission lines and radiative recombination continua. The absorption features belong to ions with, at least, three distinct ionization degrees. The lowest ionized component is slightly redshifted (v = +73 km/s) and is not in pressure equilibrium with the others, and therefore it is not likely part of the outflow, possibly belonging to the interstellar medium of the host galaxy. The other components are outflowing at velocities of -196 and -455 km/s, respectively. The source was observed simultaneously with HST-COS, finding 13 UV kinematic components. At least three of them can be kinematically associated with the observed X-ray components. Based on the HST-COS results and a previous FUSE observation, we find evidence that the UV absorbing gas might be co-located with the X-ray absorbing gas and belong to the same structure.

astro-ph.CO↗

arXiv2011

Multiwavelength campaign on Mrk 509. VI. HST/COS observations of the far-ultraviolet spectrum

We present medium resolution (R~20,000) HST/COS ultraviolet spectra covering 1155-1760 A of the Seyfert 1 Mrk 509 obtained simultaneously with a Chandra/LETGS spectrum as part of a multiwavelength campaign in 2009 that included observations with XMM-Newton, SWIFT, and Integral. Our high S/N spectrum detects additional complexity in the absorption troughs from a variety of sources in Mrk 509, including the outflow from the active nucleus, the ISM and halo of the host galaxy, and infalling clouds or stripped gas from a merger that are illuminated by the AGN. Variability between the STIS and COS observation of the -400 km/s component allows us to set an upper limit on its distance of < 250 pc. Similarly, variability of a component at +150 km/s between two prior FUSE observations limits its distance to < 1.5 kpc. The UV absorption only partially covers the emission from the AGN nucleus. Covering fractions are lower than those previously seen with STIS, and are comparable to those seen with FUSE. Given the larger apertures of COS and FUSE compared to STIS, we favor scattered light from an extended region near the AGN as the explanation for the partial covering. As observed in prior X-ray and UV spectra, the UV absorption has velocities comparable to the X-ray absorption, but the bulk of the ultraviolet absorption is in a lower ionization state with lower total column density than the gas responsible for the X-ray absorption. We conclude that the outflow from the active nucleus is a multiphase wind.

astro-ph.CO↗

arXiv2011

XMM-Newton X-ray and UV observations of the fast nova V2491 Cyg during the supersoft source phase

Two XMM observations of the fast classical nova V2491Cyg were carried out on days 39.93 and 49.62 after discovery, during the supersoft source (SSS) phase, yielding simultaneous X-ray and UV light curves and high-resolution X-ray spectra. The first X-ray light curve is highly variable with periodic oscillations (37.2 min) after an extended dip of factor of three lasting ~3 hours. The cause of the dip is currently unexplained and could have the same origin as similar events in V4743Sgr and RSOph, as it occurred on the same time scale. The 37-min period is not present during the dip and also not in the second observation. The UV light curves are variable but contain no dips and no period. High-resolution X-ray spectra are presented for 4 intervals of different intensity. All spectra are atmospheric continua with absorption lines and absorption edges. Interstellar lines of OI and NI are seen at their rest wavelengths, and a large number of high-ionization absorption lines are found at blue shifts indicating an expansion velocity of 3000-3400 km/s, which does not change significantly during the epochs of observation. Comparisons with the slower nova V4743Sgr and the symbiotic recurrent nova RSOph are presented. The SSS spectrum of V4743Sgr is much softer with broader and more complex photospheric absorption lines. Meanwhile, the absorption lines in RSOph are as narrow as in V2491Cyg, but they are less blue shifted. A remarkable similarity in the continua of V2491Cyg and RSOph is found. The only differences are smaller line shifts and additional emission lines in RSOph that are related to a dense stellar wind from the evolved companion. Three unidentified absorption lines are present in the X-ray spectra of all three novae, with rest wavelengths 26.05AA, 29.45AA, and 30.0AA. No satisfactory spectral model is currently available for the soft X-ray spectra of novae in outburst.

astro-ph.HE↗

arXiv2010

Genetic Classification of Populations using Supervised Learning

There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed \emph{unsupervised}. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available. In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

q-bio.QM↗