Wood Anatomy of Sabiaceae (S.L.)

Quantitative and qualitative data were offered for 30 taxa of Meliosma and one species each of Ophiocaryon and Sabia; qualitative data were available for additional species of Meliosma and Sabia. For a small family restricted to mesic sites, Sabiaceae had a wide range of wood anatomical expressions (e.g., long scalariform to simple perforation plates; heterocellular to homocellular multiseriate rays; tracheids, fiber-tracheids, or libriform fibers as imperforate tracheary elements; presence or absence of silica bodies and calcium oxalate crystals in rays). Growth ring type, vessel diameter, vessel density, and vessel element length were sensitively related to ecology, but to degree of winter cold rather than to aridity. Ophiocaryon differed somewhat from all or most species of Meliosma in quantitative features, but the genera agreed in qualitative features. Some authors segregate these arborescent or arboreal genera in Meliosmaceae because of distinctive features of Sabia, a liana genus; wood of lianas differs in anatomy from that of trees, and these features account for the wood differences between Sabia and Meliosma. All wood features of Sabiaceae are widespread in the genera of Rutales (Sapindales), even scalariform perforation plates. Sabiaceae are therefore best placed in Rutales, although wood of Sabiaceae is modally more primitive than that of other Rutales. Characters restricted to particular species were cited, but designation of them as diagnostic criteria was not advocated because the sampling of the family was rather incomplete

Comparative genomics approaches accurately predict deleterious variants in plants

Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another

Barley landraces are characterized by geographically heterogeneous genomic origins

<p>Genotyping data for landrace and cultivated lines from the National Small Grains Collection.</p> <p>The dataset has been devided in 11 parts. <strong>This is part 04. Make sure to download all 11 parts.</strong></p> <p>Data used in the article: "Barley landraces are characterized by geographically heterogeneous genomic origins". Published in Genome Biology</p> <p>Use the following command to put the pieces together:</p> <p>% cat * >./My_complete_data.txt</p> <p>The scripts used to analyze and plot the data are available in GitHub: https://github.com/AnaPoets/BarleyLandraces</p

ASASSN-15pz: Revealing Significant Photometric Diversity among 2009dc-like, Peculiar SNe Ia

We report comprehensive multi-wavelength observations of a peculiar Type Ia-like supernova ("SN Ia-pec") ASASSN-15pz. ASASSN-15pz is a spectroscopic "twin" of SN 2009dc, a so-called "Super-Chandrasekhar-mass" SN, throughout its evolution, but it has a peak luminosity M_B,peak = -19.69 +/- 0.12 mag that is \approx 0.6 mag dimmer and comparable to the SN 1991T sub-class of SNe Ia at the luminous end of the normal width-luminosity relation. The synthesized Ni56 mass of M_Ni56 = 1.13 +/- 0.14 M_sun is also substantially less than that found for several 2009dc-like SNe. Previous well-studied 2009dc-like SNe have generally suffered from large and uncertain amounts of host-galaxy extinction, which is negligible for ASASSN-15pz. Based on the color of ASASSN-15pz, we estimate a host extinction for SN 2009dc of E(B-V)_host=0.12 mag and confirm its high luminosity (M_B, peak[2009dc] \approx -20.3 mag). The 2009dc-like SN population, which represents ~1% of SNe Ia, exhibits a range of peak luminosities, and do not fit onto the tight width-luminosity relation. Their optical light curves also show significant diversity of late-time (>~ 50 days) decline rates. The nebular-phase spectra provide powerful diagnostics to identify the 2009dc-like events as a distinct class of SNe Ia. We suggest referring to these sources using the phenomenology-based "2009dc-like SN Ia-pec" instead of "Super-Chandrasekhar SN Ia," which is based on an uncertain theoretical interpretation.Comment: 21 pages, 16 figures, accepted for publication in Ap

The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication

The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.</p

Carnegie Supernova Project-II: Extending the Near-Infrared Hubble Diagram for Type Ia Supernovae to z∼0.1z\sim0.1

The Carnegie Supernova Project-II (CSP-II) was an NSF-funded, four-year program to obtain optical and near-infrared observations of a "Cosmology" sample of $\sim100$ Type Ia supernovae located in the smooth Hubble flow ($0.03 \lesssim z \lesssim 0.10$). Light curves were also obtained of a "Physics" sample composed of 90 nearby Type Ia supernovae at $z \leq 0.04$ selected for near-infrared spectroscopic time-series observations. The primary emphasis of the CSP-II is to use the combination of optical and near-infrared photometry to achieve a distance precision of better than 5%. In this paper, details of the supernova sample, the observational strategy, and the characteristics of the photometric data are provided. In a companion paper, the near-infrared spectroscopy component of the project is presented.Comment: 43 pages, 10 figures, accepted for publication in PAS