Phylogenetics of the Borage Family: Delimiting Boraginales and Assessing Closest Relatives

The placement of Boraginales, and relationships within the family have remained elusive in modern, broad phylogenetic studies. In order to assess the phylogeny of Boraginales, and specifically to test the sister lineage of the order, a data matrix of the chloroplast markers rbcL, ndhF, and trnL-trnF was assembled from GenBank and de novo sequences (representing 132 new GenBank accessions). Phylogenies inferred using Maximum Likelihood and Bayesian frameworks resulted in identical topologies. Tests for alternative topologies were used to assess whether any of the candidates for sister (Solanales, Gentianales, Lamiales, or Vahlia) to Boraginales could be ruled out with this dataset. Gentianales was eliminated as the possible closest relative to Boraginales. Additionally, Shimodaira-Hasegawa tests were used to test topological results within Boraginales: monophyly of Hydrophyllaceae cannot be rejected and paraphyly of Ehretiaceae with respect to the parasitic Lennoaceae is supported. Taxonomic implications are discussed within the context of these phylogenetic results

Evolution of the early to late Archean mantle from Hf-Nd-Ce isotope systematics in basalts and komatiites from the Pilbara Craton

Inferences on the early evolution of the Earth's mantle can be deduced from long-lived radiogenic isotope Lu-176-Hf-176 and systems such as Sm-147-Nd-143, for which both parent and daughter elements largely remain immobile at low metamorphic grades. However, it remains ambiguous when and to what extent mantle-crust differentiation processes had started in the Archean. For a better understanding of Archean mantle-crust evolution, we determined the initial Lu-176-Hf-176, Sm-147-Nd-143, and, in a new approach, the La-138-Ce-138 isotope compositions of a suite of Archean mafic-ultramafic rock samples from the 3.53-2.83 Ga old Pilbara Craton and 2.78-2.63 Ga old Fortescue Group in NW Australia. These rocks represent one of the best-preserved Archean successions worldwide and contain mafic-ultramafic rocks that were erupted during repeated and long-lived pulses of volcanism throughout much of the Archean. Mantlederived mafic-ultramafic rock samples were collected from six major stratigraphic groups of the Pilbara Craton and the overlying Fortescue Group in order to characterize the parental mantle source regions of the lavas and to reconstruct the temporal evolution of the ambient mantle beneath this piece of cratonic lithosphere. In addition, we analyzed contemporaneous TTG-like igneous suites and interbedded sediments in order to reconstruct the lithospheric evolution of the Pilbara Craton. The Hf-Nd-Ce isotope data imply the onset of mantle-crust differentiation in the Pilbara Craton as early as similar to 4.2 Ga, well prior to any of the preserved stratigraphy. Within error, coupled Ce-Nd-Hf isotope arrays all intersect chondritic values, implying that the Earth is of broadly chondritic composition, also for the La-138-Ce-138 isotope system. Mafic rocks usually yield strongly coupled epsilon Hf-(i), epsilon Nd-(i) and epsilon Ce-(i) values that form a mixing line between an evolving depleted upper mantle composition and the primitive mantle value (epsilon Hf-(i) ca. 0.0 to + 3.2, epsilon Nd-(i) ca. +0.2 to +1.7 and epsilon Ce-(i) ca. +0.3 to -0.1). As all Paleoarchean samples lack co-variations between Nb/Th with epsilon Hf-(i) or epsilon Nd-(i), contamination with an enriched crust is unlikely to explain this mixing trend. The most primitive mantle-like mafic samples show elevated Gd-N/Yb-N ratios (2.2-1.4), implying the involvement of a deep-rooted, near-primitive, upwelling mantle that was progressively mixed into the depleted upper mantle. In contrast to the mafic rocks, most, but not all komatiites are decoupled in their initial Hf-Nd-Ce isotope compositions, by having extremely radiogenic epsilon Hf-(i) values at only moderately high epsilon Nd-(i) and low epsilon Ce-(i) values. This decoupling is best explained by the assimilation of mantle domains that underwent early melt depletion in the garnet stability field and evolved at high Lu-176/Hf-176 ratios but at moderate Sm-147/Nd-143 and La-138/Ce-138 ratios over time. The disappearance of rocks with decoupled Hf-Nd isotope compositions after similar to 3.2 Ga is likely linked to decreasing mantle temperatures that were no longer able to melt such refractory mantle domains. Collectively, our new data for mafic rocks from the Pilbara Craton confirm the presence of long-term depleted mantle domains in the early Archean that are not sampled by the zircon Hf isotope record in the Pilbara Craton. (C) 2020 The Authors. Published by Elsevier B.V

Reader Perceptions and Impact of AI on CT Assessment of Air Trapping

Quantitative imaging measurements can be facilitated by artificial intelligence (AI) algorithms, but how they might impact decision-making and be perceived by radiologists remains uncertain. After creation of a dedicated inspiratory-expiratory CT examination and concurrent deployment of a quantitative AI algorithm for assessing air trapping, five cardiothoracic radiologists retrospectively evaluated severity of air trapping on 17 examination studies. Air trapping severity of each lobe was evaluated in three stages: qualitatively (visually); semiquantitatively, allowing manual region-of-interest measurements; and quantitatively, using results from an AI algorithm. Readers were surveyed on each case for their perceptions of the AI algorithm. The algorithm improved interreader agreement (intraclass correlation coefficients: visual, 0.28; semiquantitative, 0.40; quantitative, 0.84; P < .001) and improved correlation with pulmonary function testing (forced expiratory volume in 1 second-to-forced vital capacity ratio) (visual r = -0.26, semiquantitative r = -0.32, quantitative r = -0.44). Readers perceived moderate agreement with the AI algorithm (Likert scale average, 3.7 of 5), a mild impact on their final assessment (average, 2.6), and a neutral perception of overall utility (average, 3.5). Though the AI algorithm objectively improved interreader consistency and correlation with pulmonary function testing, individual readers did not immediately perceive this benefit, revealing a potential barrier to clinical adoption. Keywords: Technology Assessment, Quantification © RSNA, 2021

Data from: Geneious! Simplified genome skimming methods for phylogenetic systematic studies: a case study in Oreocarya (Boraginaceae)

Premise of the study: As systematists grapple with how to best harness the power of next-generation sequencing (NGS), a deluge of review papers, methods, and analytical tools make choosing the right method difficult. Oreocarya (Boraginaceae), a genus of 63 species, is a good example of a group lacking both species-level resolution and genomic resources. The use of Geneious removes bioinformatic barriers and makes NGS genome skimming accessible to even the least tech-savvy systematists. Methods: A combination of de novo and reference-guided assemblies was used to process 100-bp single-end Illumina HiSeq 2000 reads. A subset of 25 taxa was used to test the suitability of genome skimming for future systematic studies in recalcitrant lineages like Oreocarya. Results: The nuclear ribosomal cistron, the plastome, and 12 mitochondrial genes were recovered from all 25 taxa. All data processing and phylogenomic analyses were performed in Geneious. We report possible future multiplexing levels and published low-copy nuclear genes represented within de novo contigs. Discussion: Genome skimming represents a much-improved primary data collection over PCR+Sanger sequencing when chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and mitochondrial DNA (mtDNA) are the target sequences. This study details methods that plant systematists can employ to study their own taxa of interest