Intraseasonal Variations in Tropical Energy Balance: Relevance to Climate Sensitivity?

Intraseasonal variability of deep convection represents a fundamental mode of organization for tropical convection. While most studies of intraseasonal oscillations (ISOs) have focused on the spatial propagation and dynamics of convectively coupled circulations, here we examine the projection of ISOs on the tropically-averaged heat and moisture budget. One unresolved question concerns the degree to which observable variations in the "fast" processes (e.g. convection, radiative / turbulent fluxes) can inform our understanding of feedback mechanisms operable in the context of climate change. Our analysis use daily data from satellite observations, the Modern Era analysis for Research and Applications (MERRA), and other model integrations to address these questions: (i) How are tropospheric temperature variations related to that tropical deep convection and the associated ice cloud fractional amount (ICF), ice water path (IWP), and properties of warmer liquid clouds? (ii) What role does moisture transport play vis-a-vis ocean latent heat flux in enabling the evolution of deep convection to mediate PBL - free atmospheric temperature equilibration? (iii) What affect do convectively generated upper-tropospheric clouds have on the TOA radiation budget? Our methodology is similar to that of Spencer et al., (2007 GRL ) whereby a composite time series of various quantities over 60+ ISO events is built using tropical mean tropospheric temperature signal as a reference to which the variables are related at various lag times (from -30 to +30 days). The area of interest encompasses the global oceans between 20oN/S. The increase of convective precipitation cannot be sustained by evaporation within the domain, implying strong moisture transports into the tropical ocean area. The decrease in net TOA radiation that develops after the peak in deep convective rainfall, is part of the response that constitutes a "discharge" / "recharge" mechanism that facilitates tropical heat balance maintenance on these time scales. However, water vapor and hydrologic scaling relationships for this mode of variability cast doubt on the utility of ISO variations as proxies for climate sensitivity response to external radiatively forced (e.g. greenhouse gas-induced) climate change

Detection of selective sweeps in cattle using genome-wide SNP data

Background: The domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have now been identified in the genomes of many animal species including humans, dogs, horses, and chickens. Here, we attempt to identify and characterise regions of the bovine genome that have been subjected to selective sweeps.Results: Two datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 diverse cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 85 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions and the lack of sequence data for the analysed breeds precludes the nomination of selected genes or variants and limits the prediction of the selected phenotypes. However, phenotypes that we predict to have historically been under strong selection include horned-polled, coat colour, stature, ear morphology, and behaviour.Conclusions: The bias towards common SNPs in the design of the BovineSNP50 assay led to the identification of recent selective sweeps associated with breed formation and common to only a small number of breeds rather than ancient events associated with domestication which could potentially be common to all European taurines. The limited SNP density, or marker resolution, of the BovineSNP50 assay significantly impacted the rate of false discovery of selective sweeps, however, we found sweeps in common between breeds which were confirmed using an ultra-high-density assay scored in a small number of animals from a subset of the breeds. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories and the very different environmental habitats to which these sub-species have adapted.Peer reviewedAnimal Scienc

Comparison of Bayesian models to estimate direct genomic values in multi-breed commercial beef cattle

Background: While several studies have examined the accuracy of direct genomic breeding values (DGV) within and across purebred cattle populations, the accuracy of DGV in crossbred or multi-breed cattle populations has been less well examined. Interest in the use of genomic tools for both selection and management has increased within the hybrid seedstock and commercial cattle sectors and research is needed to determine their efficacy. We predicted DGV for six traits using training populations of various sizes and alternative Bayesian models for a population of 3240 crossbred animals. Our objective was to compare alternate models with different assumptions regarding the distributions of single nucleotide polymorphism (SNP) effects to determine the optimal model for enhancing feasibility of multi-breed DGV prediction for the commercial beef industry.Results: Realized accuracies ranged from 0.40 to 0.78. Randomly assigning 60 to 70% of animals to training (n is about 2000 records) yielded DGV accuracies with the smallest coefficients of variation. Mixture models (BayesB95, BayesC[pi]) and models that allow SNP effects to be sampled from distributions with unequal variances (BayesA, BayesB95) were advantageous for traits that appear or are known to be influenced by large-effect genes. For other traits, models differed little in prediction accuracy (~0.3 to 0.6%), suggesting that they are mainly controlled by small-effect loci.Conclusions: The proportion (60 to 70%) of data allocated to training that optimized DGV accuracy and minimized the coefficient of variation of accuracy was similar to large dairy populations. Larger effects were estimated for some SNPs using BayesA and BayesB95 models because they allow unequal SNP variances. This substantially increased DGV accuracy for Warner-Bratzler Shear Force, for which large-effect quantitative trait loci (QTL) are known, while no loss in accuracy was observed for traits that appear to follow the infinitesimal model. Large decreases in accuracy (up to 0.07) occurred when SNPs that presumably tag large-effect QTL were over-regressed towards the mean in BayesC0 analyses. The DGV accuracies achieved here indicate that genomic selection has predictive utility in the commercial beef industry and that using models that reflect the genomic architecture of the trait can have predictive advantages in multi-breed populations.Peer reviewedAnimal Scienc

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation

<p>Abstract</p> <p>Background</p> <p>Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction.</p> <p>Methods</p> <p>Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values.</p> <p>Results</p> <p>Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied.</p> <p>Conclusions</p> <p>These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.</p

Intraseasonal Variations in Tropical Deep Convection, Tropospheric Mean Temperature and Cloud-Induced Radiative Fluxes

Intraseasonal variability of deep convection represents a fundamental mode of variability in the organization of tropical convection. While most studies of intraseasonal oscillations (ISOs) have focused on the spatial propagation and dynamics of convectively coupled circulations, we examine the projection of ISOs on the tropically-averaged temperature and energy budget. The area of interest is the global oceans between 20oN/S. Our analysis then focuses on these questions: (i) How is tropospheric temperature related to tropical deep convection and the associated ice cloud fractional amount (ICF) and ice water path (IWP)? (ii) What is the source of moisture sustaining the convection and what role does deep convection play in mediating the PBL - free atmospheric temperature equilibration? (iii) What affect do convectively generated upper-tropospheric clouds have on the TOA radiation budget? Our methodology is similar to that of Spencer et al., (2007) with some modifications and some additional diagnostics of both clouds and boundary layer thermodynamics. A composite ISO time series of cloud, precipitation and radiation quantities built from nearly 40 events during a six-year period is referenced to the atmospheric temperature signal. The increase of convective precipitation cannot be sustained by evaporation within the domain, implying strong moisture transports into the tropical ocean area. While there is a decrease in net TOA radiation that develops after the peak in deep convective rainfall, there seems little evidence that an "Infrared Iris"- like mechanism is dominant. Rather, the cloud-induced OLR increase seems largely produced by weakened convection with warmer cloud tops. Tropical ISO events offer an accessible target for studying ISOs not just in terms of propagation mechanisms, but on their global signals of heat, moisture and radiative flux feedback processes

Relationships Between Tropical Deep Convection, Tropospheric Mean Temperature and Cloud-Induced Radiative Fluxes on Intraseasonal Time Scales

Intraseasonal variability of deep convection represents a fundamental mode of variability in the organization of tropical convection. While most studies of intraseasonal oscillations (ISOs) have focused on the spatial propagation and dynamics of convectively coupled circulations, we examine the projection of ISOs on the tropically-averaged temperature and energy budget. The area of interest is the global oceans between 20oN/S. Our analysis then focuses on these questions: (i) How is tropospheric temperature related to tropical deep convection and the associated ice cloud fractional amount (ICF) and ice water path (IWP)? (ii) What is the source of moisture sustaining the convection and what role does deep convection play in mediating the PBL - free atmospheric temperature equilibration? (iii) What affect do convectively generated upper-tropospheric clouds have on the TOA radiation budget? Our methodology is similar to that of Spencer et al., (2007) with some modifications and some additional diagnostics of both clouds and boundary layer thermodynamics. A composite ISO time series of cloud, precipitation and radiation quantities built from nearly 40 events during a six-year period is referenced to the atmospheric temperature signal. The increase of convective precipitation cannot be sustained by evaporation within the domain, implying strong moisture transports into the tropical ocean area. While there is a decrease in net TOA radiation that develops after the peak in deep convective rainfall, there seems little evidence that an "Infrared Iris"- like mechanism is dominant. Rather, the cloud-induced OLR increase seems largely produced by weakened convection with warmer cloud tops. Tropical ISO events offer an accessible target for studying ISOs not just in terms of propagation mechanisms, but on their global signals of heat, moisture and radiative flux feedback processes