Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species

Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, applications to polyploid organisms are still scarce, partly due to limited genome resources and the complexity of this system. Deep learning (DL) techniques comprise a heterogeneous collection of machine learning algorithms that have excelled at many prediction tasks. A potential advantage of DL for GP over standard linear model methods is that DL can potentially take into account all genetic interactions, including dominance and epistasis, which are expected to be of special relevance in most polyploids. In this study, we evaluated the predictive accuracy of linear and DL techniques in two important small fruits or berries: strawberry and blueberry. The two datasets contained a total of 1,358 allopolyploid strawberry (2n=8x=112) and 1,802 autopolyploid blueberry (2n=4x=48) individuals, genotyped for 9,908 and 73,045 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for five agronomic traits each. DL depends on numerous parameters that influence performance and optimizing hyperparameter values can be a critical step. Here we show that interactions between hyperparameter combinations should be expected and that the number of convolutional filters and regularization in the first layers can have an important effect on model performance. In terms of genomic prediction, we did not find an advantage of DL over linear model methods, except when the epistasis component was important. Linear Bayesian models were better than convolutional neural networks for the full additive architecture, whereas the opposite was observed under strong epistasis. However, by using a parameterization capable of taking into account these non-linear effects, Bayesian linear models can match or exceed the predictive accuracy of DL. A semiautomatic implementation of the DL pipeline is available at https://github.com/lauzingaretti/deepGP/

Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species

Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates are predicted using genome wide marker information. Although numerous examples of GP exist in plants and animals, applications to polyploid organisms are still scarce, partly due to limited genome resources and the complexity of this system. Deep learning (DL) techniques comprise a heterogeneous collection of machine learning algorithms that have excelled at many prediction tasks. A potential advantage of DL for GP over standard linear model methods is that DL can potentially take into account all genetic interactions, including dominance and epistasis, which are expected to be of special relevance in most polyploids. In this study, we evaluated the predictive accuracy of linear and DL techniques in two important small fruits or berries: strawberry and blueberry. The two datasets contained a total of 1,358 allopolyploid strawberry (2n=8x=112) and 1,802 autopolyploid blueberry (2n=4x=48) individuals, genotyped for 9,908 and 73,045 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for five agronomic traits each. DL depends on numerous parameters that influence performance and optimizing hyperparameter values can be a critical step. Here we show that interactions between hyperparameter combinations should be expected and that the number of convolutional filters and regularization in the first layers can have an important effect on model performance. In terms of genomic prediction, we did not find an advantage of DL over linear model methods, except when the epistasis component was important. Linear Bayesian models were better than convolutional neural networks for the full additive architecture, whereas the opposite was observed under strong epistasis. However, by using a parameterization capable of taking into account these non-linear effects, Bayesian linear models can match or exceed the predictive accuracy of DL. A semiautomatic implementation of the DL pipeline is available at https://github.com/lauzingaretti/deepGP/.info:eu-repo/semantics/publishedVersio

On the compact HII galaxy UM 408 as seen by GMOS-IFU: Physical conditions

We present Integral Field Unit GMOS-IFU data of the compact HII galaxy UM408, obtained at Gemini South telescope, in order to derive the spatial distribution of emission lines and line ratios, kinematics, plasma parameters, and oxygen abundances as well the integrated properties over an area of 3"x4".4(~750x1100 pc) located in the central part of the galaxy. The starburst in this area is resolved into two giant regions of ~375 and 250pc diameter, respectively. The ages of these two regions, estimated using Hb equivalent widths, suggest that they are coeval events of ~5Myr with stellar masses of ~10^4M_o. We have also used [OIII]/Hb and [SII]/Ha ratio maps to explore the excitation mechanisms in this galaxy. The Ha emission line was used to measure the radial velocity and velocity dispersion. We derived an integrated oxygen abundance of 12+log(O/H)=7.87 summing over all spaxels in our field of view. An average value of 12+log(O/H)=7.77 and a difference of D(O/H)=0.47 between the minimum and maximum values (7.58+-0.06-8.05+-0.04) were found, considering all data points where the oxygen abundance was measured. The spatial distribution of oxygen abundance does not show any significant gradient across the galaxy. On the other hand, the bulk of data points are lying in a region of +-2sigma dispersion (with sigma=0.1 dex) around the average value, confirming that this compact HII galaxy as other previously studied dwarf irregular galaxies is chemically homogeneous. Therefore, the new metals processed and injected by the current star formation episode are possibly not observed and reside in the hot gas phase, whereas the metals from previous events are well mixed and homogeneously distributed through the whole extent of the galaxy.Comment: 30 pages, 10 figures. AJ accepte

Planck intermediate results VI. The dynamical structure of PLCKG214.6+37.0, a Planck discovered triple system of galaxy clusters

The survey of galaxy clusters performed by Planck through the Sunyaev-Zeldovich effect has already discovered many interesting objects, thanks to its full sky coverage. One of the SZcandidates detected in the early months of the mission near to the signal-to-noise threshold, PLCKG214.6+37.0, was later revealed by XMM-Newton to be a triple system of galaxy clusters. We present the results from a deep XMM-Newton re-observation of PLCKG214.6+37.0, part of a multi-wavelength programme to investigate Planck discovered superclusters. The characterisation of the physical properties of the three components has allowed us to build a template model to extract the total SZ signal of this system with Planck data. We have partly reconciled the discrepancy between the expected SZ signal derived from X-rays and the observed one, which are now consistent within 1.2?. We measured the redshift of the three components with the iron lines in the X-ray spectrum, and confirm that the three clumps are likely part of the same supercluster structure. The analysis of the dynamical state of the three components, as well as the absence of detectable excess X-ray emission, suggests that we are witnessing the formation of a massive cluster at an early phase of interaction

Planck intermediate results III.The relation between galaxy cluster mass and Sunyaev-Zeldovich signal

We examine the relation between the galaxy cluster mass M and Sunyaev-Zeldovich (SZ) effect signal for a sample of 19 objects for which weak lensing (WL) mass measurements obtained from Subaru Telescope data are available in the literature. Hydrostatic X-ray masses are derived from XMM-Newton archive data, and the SZ effect signal is measured from Planck all-sky survey data. We find an relation that is consistent in slope and normalisation with previous determinations using weak lensing masses; however, there is a normalisation offset with respect to previous measures based on hydrostatic X-ray mass-proxy relations. We verify that our SZ effect measurements are in excellent agreement with previous determinations from Planck data. For the present sample, the hydrostatic X-ray masses at R500 are on average ~20 percent larger than the corresponding weak lensing masses, which is contrary to expectations. We show that the mass discrepancy is driven by a difference in mass concentration as measured by the two methods and, for the present sample, that the mass discrepancy and difference in mass concentration are especially large for disturbed systems. The mass discrepancy is also linked to the offset in centres used by the X-ray and weak lensing analyses, which again is most important in disturbed systems. We outline several approaches that are needed to help achieve convergence in cluster mass measurement with X-ray and weak lensing observations

Planck intermediate results XI. The gas content of dark matter halos: The sunyaev-zeldovich-stellar mass relation for locally brightest galaxies

We present the scaling relation between Sunyaev-Zeldovich (SZ) signal and stellar mass for almost 260,000 locally brightest galaxies (LBGs) selected from the Sloan Digital Sky Survey (SDSS). These are predominantly the central galaxies of their dark matter halos. We calibrate the stellar-to-halo mass conversion using realistic mock catalogues based on the Millennium Simulation. Applying a multi-frequency matched filter to the Planck data for each LBG, and averaging the results in bins of stellar mass, we measure the mean SZ signal down to M? ~ 2 × 1011 M?, with a clear indication of signal at even lower stellar mass. We derive the scaling relation between SZ signal and halo mass by assigning halo properties from our mock catalogues to the real LBGs and simulating the Planck observation process. This relation shows no evidence for deviation from a power law over a halo mass range extending from rich clusters down to M500 ~ 2 × 1013 M?, and there is a clear indication of signal down to M500 ~ 4 × 1012 M?. Planck?s SZdetections in such low-mass halos imply that about a quarter of all baryons have now been seen in the form of hot halo gas, and that this gas must be less concentrated than the dark matter in such halos in order to remain consistent with X-ray observations. At the high-mass end, the measured SZ signal is 20% lower than found from observations of X-ray clusters, a difference consistent with the magnitude of Malmquist bias effects that were previously estimated for the X-ray sample

Planck intermediate results IV. The XMM-Newton validation programme for new Planck galaxy clusters

We present the final results from the XMM-Newton validation follow-up of new Planck galaxy cluster candidates. We observed 15 new candidates, detected with signal-to-noise ratios between 4.0 and 6.1 in the 15.5-month nominal Planck survey. The candidates were selected using ancillary data flags derived from the ROSAT All Sky Survey (RASS) and Digitized Sky Survey all-sky maps, with the aim of pushing into the low SZ flux, high-z regime and testing RASS flags as indicators of candidate reliability. Fourteen new clusters were detected by XMM-Newton, ten single clusters and two double systems. Redshifts from X-ray spectroscopy lie in the range 0.2 to 0.9, with six clusters at z > 0.5. Estimated masses (M500) range from 2.5 × 1014 to 8 × 1014 M?. We discuss our results in the context of the full XMM-Newton validation programme, in which 51 new clusters have been detected. This includes four double and two triple systems, some of which are chance projections on the sky of clusters at different redshifts. We find thatassociation with a source from the RASS-Bright Source Catalogue is a robust indicator of the reliability of a candidate, whereas association with a source from the RASS-Faint Source Catalogue does not guarantee that the SZ candidate is a bona fide cluster. Nevertheless, most Planck clusters appear in RASS maps, with a significance greater than 2? being a good indication that the candidate is a real cluster. Candidate validation from association with SDSS galaxy overdensity at z > 0.5 is also discussed. The full sample gives a Planck sensitivity threshold of Y500 ~ 4 × 10-4 arcmin2, with indication for Malmquist bias in the YX?Y500 relation below this threshold. The corresponding mass threshold depends on redshift. Systems with M500 > 5 × 1014 M? at z > 0.5 are easily detectable with Planck. The newly-detected clusters follow the YX?Y500 relation derived from X-ray selected samples. Compared to X-ray selected clusters, the new SZ clusters have a lower X-ray luminosity on average for their mass. There is no indication of departure from standard self-similar evolution in the X-ray versus SZ scaling properties. In particular, there is no significant evolution of the YX/Y500 ratio

Planck intermediate results: II. Comparison of sunyaev-zeldovich measurements from planck and from the arcminute microkelvin imager for 11 galaxy clusters

A comparison is presented of Sunyaev-Zeldovich measurements for 11 galaxy clusters as obtained by Planck and by the ground-based interferometer, the Arcminute Microkelvin Imager. Assuming a universal spherically-symmetric Generalised Navarro, Frenk and White (GNFW) model for the cluster gas pressure profile, we jointly constrain the integrated Compton-Y parameter (Y500) and the scale radius (?500) of each cluster. Our resulting constraints in the Y500 ? ?500 2D parameter space derived from the two instruments overlap significantly for eight of the clusters, although, overall, there is a tendency for AMI to find the Sunyaev-Zeldovich signal to be smaller in angular size and fainter than Planck. Significant discrepancies exist for the three remaining clusters in the sample, namely A1413, A1914, and the newly-discovered Planck cluster PLCKESZ G139.59+24.18. The robustness of the analysis of both the Planck and AMI data is demonstrated through the use of detailed simulations, which also discount confusion from residual point (radio) sources and from diffuse astrophysical foregrounds as possible explanations for the discrepancies found. For a subset of our cluster sample, we have investigated the dependence of our results on the assumed pressure profile by repeating the analysis adopting the best-fitting GNFW profile shape which best matches X-ray observations. Adopting the best-fitting profile shape from the X-ray data does not, in general, resolve the discrepancies found in this subset of five clusters. Though based on a small sample, our results suggest that the adopted GNFW model may not be sufficiently flexible to describe clusters universally

Planck intermediate results: VIII. Filaments between interacting clusters

Context. About half of the baryons of the Universe are expected to be in the form of filaments of hot and low-density intergalactic medium. Most of these baryons remain undetected even by the most advanced X-ray observatories, which are limited in sensitivity to the diffuse low-density medium. Aims. The Planck satellite has provided hundreds of detections of the hot gas in clusters of galaxies via the thermal Sunyaev-Zel?dovich (tSZ) effect and is an ideal instrument for studying extended low-density media through the tSZ effect. In this paper we use the Planck data to search for signatures of a fraction of these missing baryons between pairs of galaxy clusters. Methods. Cluster pairs are good candidates for searching for the hotter and denser phase of the intergalactic medium (which is more easily observed through the SZ effect). Using an X-ray catalogue of clusters and the Planck data, we selected physical pairs of clusters as candidates. Using the Planck data, we constructed a local map of the tSZ effect centred on each pair of galaxy clusters. ROSAT data were used to construct X-ray maps of these pairs. After modelling and subtracting the tSZ effect and X-ray emission for each cluster in the pair, we studied the residuals on both the SZ and X-ray maps. Results. For the merging cluster pair A399-A401 we observe a significant tSZ effect signal in the intercluster region beyond the virial radii of the clusters. A joint X-ray SZ analysis allows us to constrain the temperature and density of this intercluster medium. We obtain a temperature of kT = 7.1 ± 0.9 ? keV (consistent with previous estimates) and a baryon density of (3.7 ± 0.2) × 10-4 ?cm-3. Conclusions. The Planck satellite mission has provided the first SZ detection of the hot and diffuse intercluster gas