Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae)

<p>Abstract</p> <p>Background</p> <p>The <it>Ampelopsis </it>clade (<it>Ampelopsis </it>and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a rare example to study both the Northern and the Southern Hemisphere intercontinental disjunctions. We reconstruct the temporal and spatial diversification of the <it>Ampelopsis </it>clade to explore the evolutionary processes that have resulted in their intercontinental disjunctions in six continents.</p> <p>Results</p> <p>The Bayesian molecular clock dating and the likelihood ancestral area analyses suggest that the <it>Ampelopsis </it>clade most likely originated in North America with its crown group dated at 41.2 Ma (95% HPD 23.4 - 61.0 Ma) in the middle Eocene. Two independent Laurasian migrations into Eurasia are inferred to have occurred in the early Miocene via the North Atlantic land bridges. The ancestor of the Southern Hemisphere lineage migrated from North America to South America in the early Oligocene. The Gondwanan-like pattern of intercontinental disjunction is best explained by two long-distance dispersals: once from South America to Africa estimated at 30.5 Ma (95% HPD 16.9 - 45.9 Ma), and the other from South America to Australia dated to 19.2 Ma (95% HPD 6.7 - 22.3 Ma).</p> <p>Conclusions</p> <p>The global disjunctions in the <it>Ampelopsis </it>clade are best explained by a diversification model of North American origin, two Laurasian migrations, one migration into South America, and two post-Gondwanan long-distance dispersals. These findings highlight the importance of both vicariance and long distance dispersal in shaping intercontinental disjunctions of flowering plants.</p

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated

ATHENA detector proposal - a totally hermetic electron nucleus apparatus proposed for IP6 at the Electron-Ion Collider

ATHENA has been designed as a general purpose detector capable of delivering the full scientific scope of the Electron-Ion Collider. Careful technology choices provide fine tracking and momentum resolution, high performance electromagnetic and hadronic calorimetry, hadron identification over a wide kinematic range, and near-complete hermeticity.This article describes the detector design and its expected performance in the most relevant physics channels. It includes an evaluation of detector technology choices, the technical challenges to realizing the detector and the R&D required to meet those challenges

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Figure 1 from: Wen J, Boggan J, Nie Z (2014) Synopsis of Nekemias Raf., a segregate genus from Ampelopsis Michx. (Vitaceae) disjunct between eastern/southeastern Asia and eastern North America, with ten new combinations. PhytoKeys 42: 11-19. https://doi.org/10.3897/phytokeys.42.7704

Figure 1 - Images of representative species of Nekemias Raf. A–B Nekemias arborea (L.) J. Wen & Boggan, voucher specimen: J. Wen 12005 (US), collected from Montgomery Co., Texas, USA C–D Nekemias cantoniensis (Hook. & Arn.) J. Wen & Z.L. Nie, voucher specimen: J. Wen 10613 (US), collected from Xichou Xian, Yunnan province, China E–F Nekemias celebica (Suess.) J. Wen & Boggan, voucher specimen: J. Wen 10242 (US), collected from SE Sulawesi, Indonesia

The complete plastid genome sequence of Lysidice brevicalyx (Fabaceae: Detarioideae), an arbor species endemic to China

The plastid genome of Lysidice brevicalyx was successfully assembled using Illumina sequencing reads for the first time. The complete plastid genome of L. brevicalyx is a circular structure of 159,084 bp with a GC content of 36.4%. It comprises a large single-copy (LSC) region of 87,783 bp, a small single-copy (SSC) region of 19,557 bp, and two inverted repeat regions (IRA and IRB) of 25,872 bp, each. The plastome of L. brevicalyx contains a total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. The phylogenetic analysis strongly supports the monophyly of Lysidice. This study provides the first complete plastid genome sequence of L. brevicalyx and contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species

Molecular Phylogeny of <i>Gueldenstaedtia</i> and <i>Tibetia</i> (Fabaceae) and Their Biogeographic Differentiation within Eastern Asia

<div><p><i>Tibetia</i> and <i>Gueldenstaedtia</i> are two morphologically similar and small genera in Fabaceae, with distributions largely corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms in eastern Asia, respectively. These two genera have confusing relationships based on morphology; therefore, we aimed to provide a clear understanding of their phylogenetic and biogeographic evolution within eastern Asia. In our investigations we included 88 samples representing five <i>Gueldenstaedtia</i> species, five <i>Tibetia</i> species, and outgroup species were sequenced using five markers (nuclear: ITS; chloroplast: <i>matK</i>, <i>trnL-F</i>, <i>psbA-trnH</i> and <i>rbcL</i>). Our phylogenetic results support (1) the monophyly of <i>Tibetia</i> and of <i>Gueldenstaedtia</i>, respectively; and (2) that <i>Tibetia</i> and <i>Gueldenstaedtia</i> are sister genera. Additionally, our data identified that <i>Tibetia</i> species had much higher sequence variation than <i>Gueldenstaedtia</i> species. Our results suggest that the two genera were separated from each other about 17.23 million years ago, which is congruent with the Himalayan orogeny and the uplift of the Tibetan Plateau in the mid Miocene. The divergence of <i>Tibetia</i> and <i>Gueldenstaedtia</i> is strongly supported by the separation of the Sino-Himalayan and Sino-Japanese region within eastern Asia. In addition, the habitat heterogeneity may accelerate the molecular divergence of <i>Tibetia</i> in the Sino-Himalayan region.</p></div