Diffusion Approximations for Demographic Inference: DaDi

Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia, building the most complex statistically well-characterized model of human migration out of Africa to date

Association Between Air Pollution and Low Birth Weight: A Community-Based Study

The relationship between maternal exposure to air pollution during periods of pregnancy (entire and specific periods) and birth weight was investigated in a well-defined cohort. Between 1988 and 1991, all pregnant women living in four residential areas of Beijing were registered and followed from early pregnancy until delivery. Information on individual mothers and infants was collected. Daily air pollution data were obtained independently. The sample for analysis included 74,671 first-parity live births were gestational age 37-44 weeks. Multiple linear regression and logistic regression were used to estimate the effects of air pollution on birth weight and low birth weight (< 2,500 g), adjusting for gestational age, residence, year of birth, maternal age, and infant gender. There was a significant exposure-response relationship between maternal exposures to sulfur dioxide (SO2) and total suspended particles (TSP) during the third trimester of pregnancy and infant birth weight. The adjusted odds ratio for low birth weight was 1.11 (95% CI, 1.06-1.16) for each 100 micrograms/m3 increase in SO2 and 1.10 (95% CI, 1.05-1.14) for each 100 micrograms/m3 increase in TSP. The estimated reduction in birth weight was 7.3 g and 6.9 g for each 100 micrograms/m3 increase in SO2 and in TSP, respectively. The birth weight distribution of the high-exposure group was more skewed toward the left tail (i.e., with higher proportion of births < 2,500 g) than that of the low-exposure group. Although the effects of other unmeasured risk factors cannot be excluded with certainty, our data suggests that TSP and SO2, or a more complex pollution mixture associated with these pollutants, contribute to an excess risk of low birth weight in the Beijing population.National Institute of Environmental Health Sciences (ES05947, ES08337); National Institute of Child Health & Human Development (R01 HD32505); Department of Health and Human Services (MCJ-259501, HRSA 5 T32 PE10014

Performance of Major Flare Watches from the Max Millennium Program (2001-2010)

The physical processes that trigger solar flares are not well understood and significant debate remains around processes governing particle acceleration, energy partition, and particle and energy transport. Observations at high resolution in energy, time, and space are required in multiple energy ranges over the whole course of many flares in order to build an understanding of these processes. Obtaining high-quality, co-temporal data from ground- and space- based instruments is crucial to achieving this goal and was the primary motivation for starting the Max Millennium program and Major Flare Watch (MFW) alerts, aimed at coordinating observations of all flares >X1 GOES X-ray classification (including those partially occulted by the limb). We present a review of the performance of MFWs from 1 February 2001 to 31 May 2010, inclusive, that finds: (1) 220 MFWs were issued in 3,407 days considered (6.5% duty cycle), with these occurring in 32 uninterrupted periods that typically last 2-8 days; (2) 56% of flares >X1 were caught, occurring in 19% of MFW days; (3) MFW periods ended at suitable times, but substantial gain could have been achieved in percentage of flares caught if periods had started 24 h earlier; (4) MFWs successfully forecast X-class flares with a true skill statistic (TSS) verification metric score of 0.500, that is comparable to a categorical flare/no-flare interpretation of the NOAA Space Weather Prediction Centre probabilistic forecasts (TSS = 0.488).Comment: 19 pages, 2 figures, accepted for publication in Solar Physic

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).</p