Species delimitation and phylogeny of a New Zealand plant species radiation

<p>Abstract</p> <p>Background</p> <p>Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation <it>Ourisia </it>species (Plantaginaceae) in the New Zealand archipelago.</p> <p>Results</p> <p>New Zealand <it>Ourisia </it>are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of <it>Ourisia </it>produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties.</p> <p>Conclusion</p> <p><it>Ourisia </it>radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in <it>Ourisia</it>. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.</p

The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution

<p>Abstract</p> <p>Background</p> <p>Bacteria occur in facultative association and intracellular symbiosis with a diversity of eukaryotic hosts. Recently, we have helped to characterise an intracellular nitrogen fixing bacterium, the so-called spheroid body, located within the diatom <it>Rhopalodia gibba</it>. Spheroid bodies are of cyanobacterial origin and exhibit features that suggest physiological adaptation to their intracellular life style. To investigate the genome modifications that have accompanied the process of endosymbiosis, here we compare gene structure, content and organisation in spheroid body and cyanobacterial genomes.</p> <p>Results</p> <p>Comparison of the spheroid body's genome sequence with corresponding regions of near free-living relatives indicates that multiple modifications have occurred in the endosymbiont's genome. These include localised changes that have led to elimination of some genes. This gene loss has been accompanied either by deletion of the respective DNA region or replacement with non-coding DNA that is AT rich in composition. In addition, genome modifications have led to the fusion and truncation of genes. We also report that in the spheroid body's genome there is an accumulation of deleterious mutations in genes for cell wall biosynthesis and processes controlled by transposases. Interestingly, the formation of pseudogenes in the spheroid body has occurred in the presence of intact, and presumably functional, <it>rec</it>A and <it>rec</it>F genes. This is in contrast to the situation in most investigated obligate intracellular bacterium-eukaryote symbioses, where at least either <it>rec</it>A or <it>rec</it>F has been eliminated.</p> <p>Conclusion</p> <p>Our analyses suggest highly specific targeting/loss of individual genes during the process of genome reduction and establishment of a cyanobacterial endosymbiont inside a eukaryotic cell. Our findings confirm, at the genome level, earlier speculation on the obligate intracellular status of the spheroid body in <it>Rhopalodia gibba</it>. This association is the first example of an obligate cyanobacterial symbiosis involving nitrogen fixation for which genomic data are available. It represents a new model system to study molecular adaptations of genome evolution that accompany a switch from free-living to intracellular existence.</p

Comparison of opioid prescribing by dentists in the United States and England

Importance: The United States consumes most of the opioids worldwide despite representing a small portion of the world\u27s population. Dentists are one of the most frequent US prescribers of opioids despite data suggesting that nonopioid analgesics are similarly effective for oral pain. While oral health and dentist use are generally similar between the United States and England, it is unclear how opioid prescribing by dentists varies between the 2 countries. Objective: To compare opioid prescribing by dentists in the United States and England. Design, Setting, and Participants: Cross-sectional study of prescriptions for opioids dispensed from outpatient pharmacies and health care settings between January 1 and December 31, 2016, by dentists in the United States and England. Data were analyzed from October 2018 to January 2019. Exposures: Opioids prescribed by dentists. Main Outcomes and Measures: Proportion and prescribing rates of opioid prescriptions. Results: In 2016, the proportion of prescriptions written by US dentists that were for opioids was 37 times greater than the proportion written by English dentists. In all, 22.3% of US dental prescriptions were opioids (11.4 million prescriptions) compared with 0.6% of English dental prescriptions (28 082 prescriptions) (difference, 21.7%; 95% CI, 13.8%-32.1%; P \u3c .001). Dentists in the United States also had a higher number of opioid prescriptions per 1000 population (35.4 per 1000 US population [95% CI, 25.2-48.7 per 1000 population] vs 0.5 per 1000 England population [95% CI, 0.03-3.7 per 1000 population]) and number of opioid prescriptions per dentist (58.2 prescriptions per dentist [95% CI, 44.9-75.0 prescriptions per dentist] vs 1.2 prescriptions per dentist [95% CI, 0.2-5.6 prescriptions per dentist]). While the codeine derivative dihydrocodeine was the sole opioid prescribed by English dentists, US dentists prescribed a range of opioids containing hydrocodone (62.3%), codeine (23.2%), oxycodone (9.1%), and tramadol (4.8%). Dentists in the United States also prescribed long-acting opioids (0.06% of opioids prescribed by US dentists [6425 prescriptions]). Long-acting opioids were not prescribed by English dentists. Conclusions and Relevance: This study found that in 2016, dentists in the United States prescribed opioids with significantly greater frequency than their English counterparts. Opioids with a high potential for abuse, such as oxycodone, were frequently prescribed by US dentists but not prescribed in England. These results illustrate how 1 source of opioids differs substantially in the United States vs England. To reduce dental opioid prescribing in the United States, dentists could adopt measures similar to those used in England, including national guidelines for treating dental pain that emphasize prescribing opioids conservatively

Protein-membrane interaction and fatty acid transfer from intestinal fatty acid-binding protein to membranes: Support for a multistep process

Fatty acid transfer from intestinal fatty acid-binding protein (IFABP) to phospholipid membranes occurs during protein-membrane collisions. Electrostatic interactions involving the α-helical "portal" region of the protein have been shown to be of great importance. In the present study, the role of specific lysine residues in the α-helical region of IFABP was directly examined. A series of point mutants in rat IFABP was engineered in which the lysine positive charges in this domain were eliminated or reversed. Using a fluorescence resonance energy transfer assay, we analyzed the rates and mechanism of fatty acid transfer from wild type and mutant proteins to acceptor membranes. Most of the α-helical domain mutants showed slower absolute fatty acid transfer rates to zwitterionic membranes, with substitution of one of the lysines of the α2 helix, Lys27, resulting in a particularly dramatic decrease in the fatty acid transfer rate. Sensitivity to negatively charged phospholipid membranes was also reduced, with charge reversal mutants in the α2 helix the most affected. The results support the hypothesis that the portal region undergoes a conformational change during protein-membrane interaction, which leads to release of the bound fatty acid to the membrane and that the α2 segment is of particular importance in the establishment of charge-charge interactions between IFABP and membranes. Cross-linking experiments with a phospholipid-photoactivable reagent underscored the importance of charge-charge interactions, showing that the physical interaction between wild-type intestinal fatty acid-binding protein and phospholipid membranes is enhanced by electrostatic interactions. Protein-membrane interactions were also found to be enhanced by the presence of ligand, suggesting different collisional complex structures for holo- and apo-IFABP.Instituto de Investigaciones Bioquímicas de La Plat

New World Origins of Southwest Pacific Gesneriaceae: Multiple Movements Across and Within the South Pacific

Coronanthereae is a tribe of ~20 species with a suite of unique morphological characters and a disjunct geographic distribution in the Southern Hemisphere. Three species are found in southern South America and the remainder in the southwest Pacific. It has been suggested, because of this distribution and disjunction, that Coronanthereae represents a relictual Gondwanan group from which the two major lineages in the family, the Old World Cyrtandroideae and the New World Gesnerioideae, originated. We tested this hypothesis by using phylogenetic analyses of nuclear and chloroplast DNA sequences, ancestral-area reconstruction, and molecular dating. The tribe is placed within the mostly Neotropical subfamily Gesnerioideae and comprises three lineages, treated here as subtribes. Two events of dispersal from South America explain the presence of the tribe in the South Pacific. Negriinae, newly recognized here, comprises arborescent genera: Australian Lenbrassia, New Caledonian Depanthus, and Negria from Lord Howe Island. Mitrariinae groups facultatively epiphytic Australian Fieldia with epiphytes from South America, a finding inconsistent with recent placement of Lenbrassia in synonymy of Fieldia. Coronantherinae consists of the arborescent Coronanthera from New Caledonia and the shrub Rhabdothamnus from New Zealand. Ancestral-area reconstruction and molecular dating of the clades support long-distance dispersal mechanisms, rather than Gondwanan vicariance, for explaining geographic distributions

Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform

<p>Abstract</p> <p>Background</p> <p>Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use of the polymerase chain reaction to amplify overlapping fragments from conserved gene loci. However, this approach is time consuming and can be more difficult to implement where gene organisation differs among plants. An alternative approach is to first isolate chloroplasts and then use the capacity of high-throughput sequencing to obtain complete genome sequences. We report our findings from studies of the latter approach, which used a simple chloroplast isolation procedure, multiply-primed rolling circle amplification of chloroplast DNA, Illumina Genome Analyzer II sequencing, and de novo assembly of paired-end sequence reads.</p> <p>Results</p> <p>A modified rapid chloroplast isolation protocol was used to obtain plant DNA that was enriched for chloroplast DNA, but nevertheless contained nuclear and mitochondrial DNA. Multiply-primed rolling circle amplification of this mixed template produced sufficient quantities of chloroplast DNA, even when the amount of starting material was small, and improved the template quality for Illumina Genome Analyzer II (hereafter Illumina GAII) sequencing. We demonstrate, using independent samples of karaka (<it>Corynocarpus laevigatus</it>), that there is high fidelity in the sequence obtained from this template. Although less than 20% of our sequenced reads could be mapped to chloroplast genome, it was relatively easy to assemble complete chloroplast genome sequences from the mixture of nuclear, mitochondrial and chloroplast reads.</p> <p>Conclusions</p> <p>We report successful whole genome sequencing of chloroplast DNA from karaka, obtained efficiently and with high fidelity.</p

Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

<p>Abstract</p> <p>Background</p> <p>Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. However, the predictive value of transcript profiling for inferring downstream-physiological processes has been unclear. In the present study we use shotgun proteomics to validate inferences from microarray studies regarding physiological differences in three <it>Pachycladon </it>species. We compare transcript and protein profiling and evaluate their predictive value for inferring glucosinolate chemotypes characteristic of these species.</p> <p>Results</p> <p>Evidence from heterologous microarrays and shotgun proteomics revealed differential expression of genes involved in glucosinolate hydrolysis (myrosinase-associated proteins) and biosynthesis (methylthioalkylmalate isomerase and dehydrogenase), the interconversion of carbon dioxide and bicarbonate (carbonic anhydrases), water use efficiency (ascorbate peroxidase, 2 cys peroxiredoxin, 20 kDa chloroplastic chaperonin, mitochondrial succinyl CoA ligase) and others (glutathione-S-transferase, serine racemase, vegetative storage proteins, genes related to translation and photosynthesis). Differences in glucosinolate hydrolysis products were directly confirmed. Overall, prediction of protein abundances from transcript profiles was stronger than prediction of transcript abundance from protein profiles. Protein profiles also proved to be more accurate predictors of glucosinolate profiles than transcript profiles. The similarity of species profiles for both transcripts and proteins reflected previously inferred phylogenetic relationships while glucosinolate chemotypes did not.</p> <p>Conclusions</p> <p>We have used transcript and protein profiling to predict physiological processes that evolved differently during diversification of three <it>Pachycladon </it>species. This approach has also identified candidate genes potentially important in adaptation, which are now the focus of ongoing study. Our results indicate that protein profiling provides a valuable tool for validating transcript profiles in studies of adaptive divergence.</p

Impact of the NICE guideline recommending cessation of antibiotic prophylaxis for prevention of infective endocarditis: before and after study

Objective To quantify the change in prescribing of antibiotic prophylaxis before invasive dental procedures for patients at risk of infective endocarditis, and any concurrent change in the incidence of infective endocarditis, following introduction of a clinical guideline from the National Institute for Health and Clinical Excellence (NICE) in March 2008 recommending the cessation of antibiotic prophylaxis in the United Kingdom

Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally.

BACKGROUND: Malaria in humans is caused by apicomplexan parasites belonging to 5 species of the genus Plasmodium. Infections with Plasmodium ovale are widely distributed but rarely investigated, and the resulting burden of disease is not known. Dimorphism in defined genes has led to P. ovale parasites being divided into classic and variant types. We hypothesized that these dimorphs represent distinct parasite species. METHODS: Multilocus sequence analysis of 6 genetic characters was carried out among 55 isolates from 12 African and 3 Asia-Pacific countries. RESULTS: Each genetic character displayed complete dimorphism and segregated perfectly between the 2 types. Both types were identified in samples from Ghana, Nigeria, São Tomé, Sierra Leone, and Uganda and have been described previously in Myanmar. Splitting of the 2 lineages is estimated to have occurred between 1.0 and 3.5 million years ago in hominid hosts. CONCLUSIONS: We propose that P. ovale comprises 2 nonrecombining species that are sympatric in Africa and Asia. We speculate on possible scenarios that could have led to this speciation. Furthermore, the relatively high frequency of imported cases of symptomatic P. ovale infection in the United Kingdom suggests that the morbidity caused by ovale malaria has been underestimated

Growth or decline in the Church of England during the decade of Evangelism: did the Churchmanship of the Bishop matter?

The Decade of Evangelism occupied the attention of the Church of England throughout the 1990s. The present study employs the statistics routinely published by the Church of England in order to assess two matters: the extent to which these statistics suggest that the 43 individual dioceses finished the decade in a stronger or weaker position than they had entered it and the extent to which, according to these statistics, the performance of dioceses led by bishops shaped in the Evangelical tradition differed from the performance of dioceses led by bishops shaped in the Catholic tradition. The data demonstrated that the majority of dioceses were performing less effectively at the end of the decade than at the beginning, in terms of a range of membership statistics, and that the rate of decline varied considerably from one diocese to another. The only exception to the trend was provided by the diocese of London, which experienced some growth. The data also demonstrated that little depended on the churchmanship of the diocesan bishop in shaping diocesan outcomes on the performance indicators employed in the study