Response of Laser-Induced Thermal Lens Effect at Solid Surface

Recently Kuo et al. [1,2] and Satio et al.[3] presented the surface-thermal lens (STL) technique, this novel photothermal deformation technique has attracted great attention because it is a highly sensitive, noncontact and nondestructive measurement[4–6]. In this technique, a modulated pump beam is focused on the sample surface to produce the surface deformation and a cw probe beam is incident at the deformation region. Differing from the conventional photothermal deformation techniques, the spot size of the probe beam at the sample surface is much larger than the pump beam one. Then the probe beam reflected from the surface produces a diffraction pattern at the detection plane. More recently, STL technique has been successfully applied to study the temperature dependence of the thermal conductivity of semiconductor materials[5], weak absorption of optical thin films[6] and characterization of the solid materials[7,8]. However, the mechanism of STL phenomena has not been completely understood. Most theoretical models took no account of the influence of the air-thermal lens (ATL), although some experiment showed that the air significantly affected the detected diffraction pattern[2]. In addition, it is necessary to characterize frequency responses of signals because the response is used to determine the thermal property of the solid materials[5]

Genome-wide analysis of butterfly bush in three uplands provides insights into biogeography, demography and speciation

Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B. alternifolia, the first within the family Scrophulariaceae. Whole-genome re-sequencing data from 48 populations plus morphological and petal colour reflectance data covering its full distribution range were collected. Three distinct genetic lineages of B. alternifolia were uncovered, corresponding to Himalayan, HDM and LP populations, with the last also differentiated morphologically and phenologically, indicating occurrence of allopatric speciation likely to be facilitated by geographic isolation and divergent adaptation to distinct ecological niches. Moreover, speciation with gene flow between populations from either side of a mountain barrier could be under way within LP. The current disjunctions within B. alternifolia might result from vicariance of a once widespread distribution, followed by several past contraction and expansion events, possibly linked to climate fluctuations promoted by the Kunlun-Yellow river tectonic movement. Several adaptive genes are likely to be either uniformly or diversely selected among regions, providing a footprint of local adaptations. These findings provide new insights into plant biogeography, adaptation and different processes of allopatric speciation

Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation

Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B. alternifolia, the first within the family Scrophulariaceae. Whole-genome re-sequencing data from 48 populations plus morphological and petal colour reflectance data covering its full distribution range were collected. Three distinct genetic lineages of B. alternifolia were uncovered, corresponding to Himalayan, HDM and LP populations, with the last also differentiated morphologically and phenologically, indicating occurrence of allopatric speciation likely to be facilitated by geographic isolation and divergent adaptation to distinct ecological niches. Moreover, speciation with gene flow between populations from either side of a mountain barrier could be under way within LP. The current disjunctions within B. alternifolia might result from vicariance of a once widespread distribution, followed by several past contraction and expansion events, possibly linked to climate fluctuations promoted by the Kunlun–Yellow river tectonic movement. Several adaptive genes are likely to be either uniformly or diversely selected among regions, providing a footprint of local adaptations. These findings provide new insights into plant biogeography, adaptation and different processes of allopatric speciation.Supplementary Material 1: Dataset S1 Morphological measurement and floral colour reflectance data for populations of Buddleja alternifola. Fig. S1 Phylogenetic trees inferred by ASTRAL- and ML-based approaches. Fig. S2 Patterns of linkage disequilibrium (LD). Fig. S3 Models 1–3, during the process of divergence among the three linkages, no gene flows with no changes in effective population size and (Model 1); with changes in effective population sizes starting from the divergence of TB (TDIV1), as well as SC and HT (TDIV2, Model 2); with changes in effective population sizes starting from TDIV1. Fig. S4 The phylogenomic tree used for time assignment of divergence for ancestral area reconstruction using representative samples of B. alternifolia and three species in the genus are currently available with re-sequencing data. Fig. S5 Cross-validation (CV) error and marginal likelihood values for different model K. Fig. S6 Reconstructing the phylogenomic relationships for 46 species of Buddleja using single-copy genes. Methods S1 Site ancestral state estimation. Methods S2 Estimating mutation rate of B. alternifolia. Methods S3 Reconstructing the phylogenomic relationships for 46 species of Buddleja using single-copy genes.Supplementary Material 2: Notes S1 Reproducibility of analyses for BEAST and r8s files.Supplementary Material 3: Table S1 Statistics of all assemblies. Table S2 Basic information with regards to genomes of 17 plants that were used to gene family analysis and the phylogenetic tree construction. Table S3 A matrix information on geographic distances among populations. Table S4 Environmental parameters used for assessment of ecological niche differentiation in B. alternifolia. Table S5 Geographical coordinate of B. alternifolia. Table S6 WGS-PacBio sequencing statistics. Table S7 WGS Illumina sequencing statistics. Table S8 HiC sequencing statistics. Table S9 Repeat annotations of the Buddleja alternifolia genome assembly. Table S10 Gene annotation statistics of the Buddleja alternifolia assembly. Table S11 Functional annotation of predicted genes in the Buddleja alternifolia genome. Table S12 Summary of the gene family analyses. Table S13 Basic information on location and genome mapping characteristics of all sampled individuals. Table S14 Summary of SNP annotations. Table S15 Global pairwise Fst between areas at the whole-genome level. Table S16 Pairwise Fst between areas in the divided nine subgroups of the whole genome, that is, eight in the gene region and one in the intergene region. Table S17 Results of nine models used in the fastsimocal analysis. Table S18 Basic parameters of three models compared in BioGeoBears, that is, Dec and Divalike based on dispersal-vicariance analysis, and Bayarea based on Bayesian inference of historical biogeography for discrete areas, with and without the founder-event speciation ‘J’ parameter. Table S19 Results of IBD and IBA analysis using simple and partial Mantel tests. Table S20 Shared genes detected by both approaches, red colour font indicating the shared genes of a significant overrepresentation with a specific GO term (P < 0.05). Table S21 Annotation of genes with significant GO terms (P < 0.05) detected by both approaches. Please note: Wiley Blackwell are not responsible for the content or functionality of any Supporting Information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office.National Natural Science Foundation of China; Second Tibetan Plateau Scientific Expedition and Research Programme; Yunnan Science and Technology Innovation Team Programme for PSESP Conservation and Utilisation; Youth Innovation Promotion Association, Chinese Academy of Sciences.https://nph.onlinelibrary.wiley.com/journal/14698137am2022BiochemistryGeneticsMicrobiology and Plant Patholog

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

The Sloan Digital Sky Survey (SDSS) started a new phase in August 2008, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Ly alpha forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg^2 in the Southern Galactic Cap, bringing the total footprint of the SDSS imaging to 14,555 deg^2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Evolution (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameters pipeline, which has better determination of metallicity for high metallicity stars.Comment: Astrophysical Journal Supplements, in press (minor updates from submitted version

High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, yet its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81,587 markers scoring 30,155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome-specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years, and use this information to conduct a genome wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker-assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analyzed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat

High-density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, yet its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81,587 markers scoring 30,155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome-specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years, and use this information to conduct a genome wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker-assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analyzed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat

Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae)

<p>Abstract</p> <p>Background</p> <p>The genus <it>Cuscuta </it>L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context.</p> <p>Results</p> <p>Here we present a well-supported phylogeny of <it>Cuscuta </it>using sequences of the nuclear ribosomal internal transcribed spacer and plastid <it>rps2</it>, <it>rbcL </it>and <it>matK </it>from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus <it>Cuscuta </it>is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with <it>rbcL </it>exhibiting even higher levels of purifying selection in <it>Cuscuta </it>than photosynthetic relatives. Nuclear genome size is highly variable within <it>Cuscuta</it>, particularly within subgenus <it>Grammica</it>, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species.</p> <p>Conclusion</p> <p>Some morphological characters traditionally used to define major taxonomic splits within <it>Cuscuta </it>are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of <it>Cuscuta </it>retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America.</p