Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution.By using chloroplast genome data from angiosperms and by taking account of new paleontological evidence, we now show that episodic rate acceleration both in terms of non-synonymous and synonymous substitutions occurred in the common ancestral branch of the core Poaceae (a group formed by rice, wheat, maize, and their allies) accompanied by adaptive evolution in several chloroplast proteins, while the rate reverted to the slow rate typical of most monocot species in the terminal branches.Our finding of episodic rate acceleration in the ancestral grasses accompanied by adaptive molecular evolution has a profound bearing on the evolution of grasses, which form a highly successful group of plants. The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages. However, the assumption is proved to be inadequate in approximating the episodic rate acceleration in the ancestral grasses, and the assumption of independent rates is more appropriate. This finding has implications for studies of molecular evolutionary rates and time-scale of evolution in other groups of organisms

Antibiotic use on paediatric inpatients in a teaching hospital in the Gambia, a retrospective study

Background: Antibiotics are useful but increasing resistance is a major problem. Our objectives were to assess antibiotic use and microbiology testing in hospitalized children in the Gambia. Methods: We conducted a retrospective analysis of paediatric inpatient data at The Edward Francis Small Teaching Hospital in Banjul, The Gambia. We extracted relevant data from the admission folders of all patients (aged >28 days to 15 years) admitted in 2015 (January-December), who received at least one antibiotic for 24 h. We also reviewed the microbiology laboratory record book to obtain separate data for the bacterial isolates and resistance test results of all the paediatric inpatients during the study period. Results: Over half of the admitted patients received at least one antibiotic during admission (496/917) with a total consumption of 670.7 Days of Antibiotic Therapy/1000 Patient-Days. The clinical diagnoses included an infectious disease for 398/496, 80.2% of the patients on antibiotics, pneumonia being the most common (184/496, 37.1%). There were 51 clinically relevant bacterial isolates, Klebsiella species being the most common (12/51, 23.5%), mainly from urine (11/12, 91.7%). Antibiotic resistance was mainly to ampicillin (38/51, 74.5%), mainly reported as Coliform species 11/51, 21.6%. Conclusions: More than half of the admitted patients received antibiotics. The reported antibiotic resistance was highest to the most commonly used antibiotics such as ampicillin. Efforts to maximize definitive antibiotic indication such as microbiological testing prior to start of antibiotics should be encouraged where possible for a more rational antibiotic use

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

Background: Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L.) Delile and the eelgrass Zostera marina L., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat. Results: In our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marina and P. oceanica) and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis. Conclusions: These results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence

First evidence for a massive extinction event affecting bees close to the K-T boundary

Bees and eudicot plants both arose in the mid-late Cretaceous, and their co-evolutionary relationships have often been assumed as an important element in the rise of flowering plants. Given the near-complete dependence of bees on eudicots we would expect that major extinction events affecting the latter would have also impacted bees. However, given the very patchy distribution of bees in the fossil record, identifying any such extinctions using fossils is very problematic. Here we use molecular phylogenetic analyses to show that one bee group, the Xylocopinae, originated in the mid-Cretaceous, coinciding with the early radiation of the eudicots. Lineage through time analyses for this bee subfamily show very early diversification, followed by a long period of seemingly no radiation and then followed by rapid diversification in each of the four constituent tribes. These patterns are consistent with both a long-fuse model of radiation and a massive extinction event close to the K-T boundary. We argue that massive extinction is much more plausible than a long fuse, given the historical biogeography of these bees and the diversity of ecological niches that they occupy. Our results suggest that events near the K-T boundary would have disrupted many plant-bee relationships, with major consequences for the subsequent evolution of eudicots and their pollinators.Sandra M. Rehan, Remko Leys, Michael P. Schwar