Repeated Origin of Three-Dimensional Leaf Venation Releases Constraints on the Evolution of Succulence in Plants

SummarySucculent water storage is a prominent feature among plants adapted to arid zones, but we know little about how succulence evolves and how it is integrated into organs already tasked with multiple functions. Increased volume in succulent leaves, for example, may result in longer transport distances between veins and the cells that they supply, which in turn could negatively impact photosynthesis [1–4]. We quantified water storage [5] in a group of 83 closely related species to examine the evolutionary dynamics of succulence and leaf venation. In most leaves, vein density decreased with increasing succulence, resulting in significant increases in the path length of water from veins to evaporative surfaces. The most succulent leaves, however, had a distinct three-dimensional (3D) venation pattern, which evolved 11–12 times within this small lineage, likely via multiple developmental pathways. 3D venation “resets” internal leaf distances, maintaining moderate vein density in extremely succulent tissues and suggesting that the evolution of extreme succulence is constrained by the need to maintain an efficient leaf hydraulic system. The repeated evolution of 3D venation decouples leaf water storage from hydraulic path length, facilitating the evolutionary exploration of novel phenotypic space

Use of swivel desks and aisle space to promote interaction in mid-sized college classrooms

Traditional designs for most mid-sized college classrooms discourage 1) face-to-face interaction among students, 2) instructor movement in the classroom, and 3) efficient transitions between different kinds of learning activities. An experimental classroom piloted during Spring Semester 2011 at the University of North Carolina at Chapel Hill uses clusters of stationary desks that swivel 360-degrees and aisle space to address these challenges. The findings from a study involving ten courses taught in the room suggest that there is a need for designs that not only promote quality interactions but also facilitate movement between small group work, class discussion, and lecture

Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling

Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler and illustrate its application to the bacteriophage PhiX174.Comment: 17 pages, 5 figure

Molecular Dating, Evolutionary Rates, and the Age of the Grasses

Many questions in evolutionary biology require an estimate of divergence times but, for groups with a sparse fossil record, such estimates rely heavily on molecular dating methods. The accuracy of these methods depends on both an adequate underlying model and the appropriate implementation of fossil evidence as calibration points. We explore the effect of these in Poaceae (grasses), a diverse plant lineage with a very limited fossil record, focusing particularly on dating the early divergences in the group. We show that molecular dating based on a data set of plastid markers is strongly dependent on the model assumptions. In particular, an acceleration of evolutionary rates at the base of Poaceae followed by a deceleration in the descendants strongly biases methods that assume an autocorrelation of rates. This problem can be circumvented by using markers that have lower rate variation, and we show that phylogenetic markers extracted from complete nuclear genomes can be a useful complement to the more commonly used plastid markers. However, estimates of divergence times remain strongly affected by different implementations of fossil calibration points. Analyses calibrated with only macrofossils lead to estimates for the age of core Poaceae ∼51-55 Ma, but the inclusion of microfossil evidence pushes this age to 74-82 Ma and leads to lower estimated evolutionary rates in grasses. These results emphasize the importance of considering markers from multiple genomes and alternative fossil placements when addressing evolutionary issues that depend on ages estimated for important group

Long-term perspectives on terrestrial and aquatic carbon cycling from palaeolimnology

Lakes are active processors and collectors of carbon (C) and thus recognized as quantitatively important within the terrestrial C cycle. Better integration of palaeolimnology (lake sediment core analyses) with limnological or modelling approaches has the potential to enhance understanding of lacustrine C processing and sequestration. Palaeolimnology simultaneously assimilates materials from across lake habitats, terrestrial watersheds and airsheds to provide a uniquely broad overview of the terrestrial-atmospheric-aquatic linkages across spatial scales. The examination of past changes over decadal-millenial timescales via palaeolimnology can inform understanding and prediction of future changes in C cycling. With a particular, but not exclusive, focus on northern latitudes we examine the methodological approaches of palaeolimnology, focusing on how relatively standard and well tested techniques might be applied to address questions of relevance to the C cycle. We consider how palaeolimnology, limnology and sedimentation studies might be linked to provide more quantitative and holistic estimates lake C cycling. Finally, we use palaeolimnological examples to consider how changes such as terrestrial vegetation cover, permafrost thaw, the formation of new lakes and reservoirs, hydrological modification of inorganic C processing, land use change, soil erosion and disruption to global nitrogen and phosphorus cycles might influence lake C cycling

The Vermont oxford neonatal encephalopathy registry: Rationale, methods, and initial results

BACKGROUND: In 2006, the Vermont Oxford Network (VON) established the Neonatal Encephalopathy Registry (NER) to characterize infants born with neonatal encephalopathy, describe evaluations and medical treatments, monitor hypothermic therapy (HT) dissemination, define clinical research questions, and identify opportunities for improved care. METHODS: Eligible infants were ≥ 36 weeks with seizures, altered consciousness (stupor, coma) during the first 72 hours of life, a 5 minute Apgar score of ≤ 3, or receiving HT. Infants with central nervous system birth defects were excluded. RESULTS: From 2006–2010, 95 centers registered 4232 infants. Of those, 59% suffered a seizure, 50% had a 5 minute Apgar score of ≤ 3, 38% received HT, and 18% had stupor/coma documented on neurologic exam. Some infants experienced more than one eligibility criterion. Only 53% had a cord gas obtained and only 63% had a blood gas obtained within 24 hours of birth, important components for determining HT eligibility. Sixty-four percent received ventilator support, 65% received anticonvulsants, 66% had a head MRI, 23% had a cranial CT, 67% had a full channel encephalogram (EEG) and 33% amplitude integrated EEG. Of all infants, 87% survived. CONCLUSIONS: The VON NER describes the heterogeneous population of infants with NE, the subset that received HT, their patterns of care, and outcomes. The optimal routine care of infants with neonatal encephalopathy is unknown. The registry method is well suited to identify opportunities for improvement in the care of infants affected by NE and study interventions such as HT as they are implemented in clinical practice

Multiple photosynthetic transitions, polyploidy, and lateral gene transfer in the grass subtribe Neurachninae

The Neurachninae is the only grass lineage known to contain C3, C4, and C3–C4 intermediate species, and as such has been suggested as a model system for studies of photosynthetic pathway evolution in the Poaceae; however, a lack of a robust phylogenetic framework has hindered this possibility. In this study, plastid and nuclear markers were used to reconstruct evolutionary relationships among Neurachninae species. In addition, photosynthetic types were determined with carbon isotope ratios, and genome sizes with flow cytometry. A high frequency of autopolyploidy was found in the Neurachninae, including in Neurachne munroi F.Muell. and Paraneurachne muelleri S.T.Blake, which independently evolved C4 photosynthesis. Phylogenetic analyses also showed that following their separate C4 origins, these two taxa exchanged a gene encoding the C4 form of phosphoenolpyruvate carboxylase. The C3–C4 intermediate Neurachne minor S.T.Blake is phylogenetically distinct from the two C4 lineages, indicating that intermediacy in this species evolved separately from transitional stages preceding C4 origins. The Neurachninae shows a substantial capacity to evolve new photosynthetic pathways repeatedly. Enablers of these transitions might include anatomical pre-conditions in the C3 ancestor, and frequent autopolyploidization. Transfer of key C4 genetic elements between independently evolved C4 taxa may have also facilitated a rapid adaptation of photosynthesis in these grasses that had to survive in the harsh climate appearing during the late Pliocene in Australia

Comet C/2004 Q2 (MACHHOLZ): Parent Volatiles, a Search for Deuterated Methane, and Constraint on the CH4 Spin Temperature

High-dispersion (l/dl ~ 25,000) infrared spectra of Comet C/2004 Q2 (Machholz) were acquired on Nov. 28-29, 2004, and Jan. 19, 2005 (UT dates) with NIRSPEC at the Keck-2 telescope on Mauna Kea. We detected H2O, CH4, C2H2, C2H6, CO, H2CO, CH3OH, HCN, and NH3 and we conducted a sensitive search for CH3D. We report rotational temperatures, production rates, and mixing ratios (with respect to H2O) at heliocentric distances of 1.49 AU (Nov. 2004) and 1.21 AU (Jan. 2005). We highlight three principal results: (1) The mixing ratios of parent volatiles measured at 1.49 AU and 1.21 AU agree within confidence limits, consistent with homogeneous composition in the mean volatile release from the nucleus of C/2004 Q2. Notably, the relative abundance of C2H6/C2H2 is substantially higher than those measured in other comets, while the mixing ratios C2H6/H2O, CH3OH/H2O, and HCN/H2O are similar to those observed in comets, referred to as "organics-normal". (2) The spin temperature of CH4 is > 35-38 K, an estimate consistent with the more robust spin temperature found for H2O. (3) We obtained a 3s upper limit of CH3D/CH4 < 0.020 (D/H < 0.005). This limit suggests that methane released from the nucleus of C/2004 Q2 is not dominated by a component formed in extremely cold (near 10 K) environments. Formation pathways of both interstellar and nebular origin consistent with the measured D/H in methane are discussed. Evaluating the relative contributions of these pathways requires further modeling of chemistry including both gas-phase and gas-grain processes in the natal interstellar cloud and in the protoplanetary disk.Comment: Accepted by The Astrophysical Journa

The Peculiar Volatile Composition of Comet 8P/Tuttle: A Contact Binary of Chemically Distinct Cometesimals?

We report measurements of eight native (i.e., released directly from the comet nucleus) volatiles (H2O, HCN, CH4, C2H2, C2H6, CO, H2CO, and CH3OH) in comet 8P/Tuttle using NIRSPEC at Keck 2. Comet Tuttle reveals a truly unusual composition, distinct from that of any comet observed to date at infrared wavelengths. The prominent enrichment of methanol relative to water contrasts the depletions of other molecules, especially C2H2 and HCN. We suggest that the nucleus of 8P/Tuttle may contain two cometesimals characterized by distinct volatile composition. The relative abundances C2/CN, C2/OH, and CN/OH in 8P/Tuttle (measured at optical/near-UV wavelengths) differ substantially from the mixing ratios of their potential parents (C2H2/HCN, C2H2/H2O, and HCN/H2O) found in this work. Based on this comparison, our results do not support C2H2 and HCN being the principal precursors for respectively C2 and CN in Tuttle. The peculiar native composition observed in 8P/Tuttle (compared to other comets) provides new strong evidence for chemical diversity in the volatile materials stored in comet nuclei. We discuss the implications of this diversity for expected variations in the deuterium enrichment of water among comets.Comment: Accepted for Astrophysical Journal Letter

Diversification in evolutionary arenas : Assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology and ecology. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a general framework for estimating rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thus d~a,b,c. We refer to the four components (a-d) and their interactions collectively as the &#039;Evolutionary Arena&#039;. We outline analytical approaches to this conceptual model that open up new avenues for research, and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples based on existing literature: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating fragmentation due to climatic oscillation; oceanic island radiations in the context of archipelago isolation and island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that large niches, lack of competition, and high-rates of niche evolution differentially promote diversification, but these results go further by quantifying the statistical interactions between variables representing these three drivers. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework results in highlighting gaps in current knowledge, and thus help to identify future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge