The Type Ia Supernova Rate in Redshift 0.5--0.9 Galaxy Clusters

Supernova (SN) rates are potentially powerful diagnostics of metal enrichment and SN physics, particularly in galaxy clusters with their deep, metal-retaining potentials and relatively simple star-formation histories. We have carried out a survey for supernovae (SNe) in galaxy clusters, at a redshift range 0.5<z<0.9, using the Advanced Camera for Surveys (ACS) on the Hubble Space Telescope. We reimaged a sample of 15 clusters that were previously imaged by ACS, thus obtaining two to three epochs per cluster, in which we discovered five likely cluster SNe, six possible cluster SNe Ia, two hostless SN candidates, and several background and foreground events. Keck spectra of the host galaxies were obtained to establish cluster membership. We conducted detailed efficiency simulations, and measured the stellar luminosities of the clusters using Subaru images. We derive a cluster SN rate of 0.35 SNuB +0.17/-0.12 (statistical) \pm0.13 (classification) \pm0.01 (systematic) [where SNuB = SNe (100 yr 10^10 L_B_sun)^-1] and 0.112 SNuM +0.055/-0.039 (statistical) \pm0.042 (classification) \pm0.005 (systematic) [where SNuM = SNe (100 yr 10^10 M_sun)^-1]. As in previous measurements of cluster SN rates, the uncertainties are dominated by small-number statistics. The SN rate in this redshift bin is consistent with the SN rate in clusters at lower redshifts (to within the uncertainties), and shows that there is, at most, only a slight increase of cluster SN rate with increasing redshift. The low and fairly constant SN Ia rate out to z~1 implies that the bulk of the iron mass in clusters was already in place by z~1. The recently observed doubling of iron abundances in the intracluster medium between z=1 and 0, if real, is likely the result of redistribution of existing iron, rather than new production of iron.Comment: Accepted to ApJ. Full resolution version available at http://kicp.uchicago.edu/~kerens/HSTclusterSNe

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

<p>Abstract</p> <p>Background</p> <p>Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.</p> <p>Results</p> <p>Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 <it>in silico </it>SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry.</p> <p>Conclusions</p> <p>The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.</p

A chromosome‐scale reference of Chenopodium watsonii helps elucidate relationships within the North American A‐genome Chenopodium species and with quinoa

Abstract Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free‐living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A‐genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence‐match similarities with quinoa, along with its well‐established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome‐scale scaffolds and 93.9% Benchmarking Universal Single‐Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A‐subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single‐nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H‐genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A‐genome sequences from the ATGC. We also present evidence for long‐range dispersal of Chenopodium diploids between North and South America

How Large Are the Effects from Changes in Family Environment? A Study of Korean American Adoptees

I analyze a new set of data on Korean American adoptees who were quasirandomly assigned to adoptive families. I find large effects on adoptees' education, income, and health from assignment to parents with more education and from assignment to smaller families. Parental education and family size are significantly more correlated with adoptee outcomes than are parental income or neighborhood characteristics. Outcomes such as drinking, smoking, and the selectivity of college attended are more determined by nurture than is educational attainment. Using the standard behavioral genetics variance decomposition, I find that shared family environment explains 14 percent of the variation in educational attainment, 35 percent of the variation in college selectivity, and 33 percent of the variation in drinking behavior. Copyright by the President and Fellows of Harvard College and the Massachusetts Institute of Technology.