Maize HapMap2 identifies extant variation from a genome in flux

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.     

Polygenic susceptibility to breast cancer and implications for prevention

The knowledge of human genetic variation that will come from the human genome sequence makes feasible a polygenic approach to disease prevention, in which it will be possible to identify individuals as susceptible by their genotype profile and to prevent disease by targeting interventions to those at risk. There is doubt, however, regarding the magnitude of these genetic effects and thus the potential to apply them to either individuals or populations. We have therefore examined the potential for prediction of risk based on common genetic variation using data from a population-based series of individuals with breast cancer. The data are compatible with a log-normal distribution of genetic risk in the population that is sufficiently wide to provide useful discrimination of high- and low-risk groups. Assuming all of the susceptibility genes could be identified, the half of the population at highest risk would account for 88% of all affected individuals. By contrast, if currently identified risk factors for breast cancer were used to stratify the population, the half of the population at highest risk would account for only 62% of all cases. These results suggest that the construction and use of genetic-risk profiles may provide significant improvements in the efficacy of population-based programs of intervention for cancers and other diseases.     

Predictive ability and economic gains from volatility forecast combinations

The availability of numerous modeling approaches for volatility forecasting leads to model uncertainty for both researchers and practitioners. A large number of studies provide evidence in favor of combination methods for forecasting a variety of financial variables, but most of them are implemented on returns forecasting and evaluate their performance based solely on statistical evaluation criteria. In this paper, we combine various volatility forecasts based on different combination schemes and evaluate their performance in forecasting the volatility of the S&P 500 index. We use an exhaustive variety of combination methods to forecast volatility, ranging from simple techniques to time-varying techniques based on the past performance of the single models and regression techniques. We then evaluate the forecasting performance of single and combination volatility forecasts based on both statistical and economic loss functions. The empirical analysis in this paper yields an important conclusion. Although combination forecasts based on more complex methods perform better than the simple combinations and single models, there is no dominant combination technique that outperforms the rest in both statistical and economic terms.     

Soil water and temperature response to prescribed burning

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