Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

<p>Abstract</p> <p>Background</p> <p>Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?</p> <p>Results</p> <p>We reconstruct the infrageneric phylogeny of <it>Pinus </it>from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve <it>Pinus</it>, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (<it>ycf</it>1, <it>ycf</it>2), highlighting their unusual evolutionary properties.</p> <p>Conclusion</p> <p>Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.</p

Distributed Modeling of Ablation (1996–2011) and Climate Sensitivity on the Glaciers of Taylor Valley, Antarctica

The McMurdo Dry Valleys of Antarctica host the coldest and driest ecosystem on Earth, which is acutely sensitive to the availability of water coming from glacial runoff. We modeled the spatial variability in ablation and assessed climate sensitivity of the glacier ablation zones using 16 years of meteorological and surface mass-balance observations collected in Taylor Valley. Sublimation was the primary form of mass loss over much of the ablation zones, except for near the termini where melt, primarily below the surface, dominated. Microclimates in ~10 m scale topographic basins generated melt rates up to ten times higher than over smooth glacier surfaces. In contrast, the vertical terminal cliffs on the glaciers can have higher or lower melt rates than the horizontal surfaces due to differences in incoming solar radiation. The model systematically underpredicted ablation for the final 5 years studied, possibly due to an increase of windblown sediment. Surface mass-balance sensitivity to temperature was ~−0.02 m w.e. K−1, which is among the smallest magnitudes observed globally. We also identified a high sensitivity to ice albedo, with a decrease of 0.02 having similar effects as a 1 K increase in temperature, and a complex sensitivity to wind speed

Dancing Against falls iN Community-dwElling older adults (DANCE):a study protocol of a stratified, block-randomised trial

BACKGROUND: Unintentional falls among older adults are of primary importance due to their impact on quality of life. Falling accounts for 95% of hip fractures, leading to an approximately six times increased risk of death within the first 3 months. Furthermore, physical and cognitive parameters are risk factors for falls. The purpose of this study is to examine the effect of a 6-month salsa dance training intervention, compared with regular fitness circuit training and a control group. METHODS: This study will include 180 older adults: 90 healthy patients and 90 patients with osteoporosis. Participants will be allocated randomly in either of the groups, stratified according to age. Training groups will receive 2 weekly 1-hour training sessions, continuously through 6 months. Participants will be tested at baseline and 6 and 18 months post baseline. Primary outcome will be number of falls and secondary outcomes include bone mineral density, body composition, pain evaluation, weekly physical activity, single-task and dual-task gait patterns, balance, Fullerton Functional Fitness Test and assessment of the mini-BESTest. DISCUSSION: This study will investigate the effects of a specially designed dance training programme (Dancing Against falls iN Community-dwElling older adults (DANCE)) to reduce the risk of falling among older adults. The study will investigate the effect against an active and passive comparator, resulting in the possibility to state, if DANCE training should be an alternative to traditional training. TRIAL REGISTRATION NUMBER: NCT03683849

Finding a (Pine) Needle in a Haystack: Chloroplast Genome Sequence Divergence in Rare and Widespread Pines

Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world\u27s rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants

Near-Surface Internal Melting: a Substantial Mass Loss on Antarctic Dry Valley Glaciers

The McMurdo Dry Valleys, southern Victoria Land, East Antarctica, are a polar desert, and melt from glacial ice is the primary source of water to streams, lakes and associated ecosystems. Previous work found that to adequately model glacier ablation and subsurface ice temperatures with a surface energy-balance model required including the transmission of solar radiation into the ice. Here we investigate the contribution of subsurface melt to the mass balance of (and runoff from) Dry Valley glaciers by including a drainage process in the model and applying the model to three glacier sites using 13years of hourly meteorological data. Model results for the smooth glacier surfaces common to many glaciers in the Dry Valleys showed that sublimation was typically the largest component of surface lowering, with rare episodes of surface melting, consistent with anecdotal field observations. Results also showed extensive internal melting 5-15 cm below the ice surface, the drainage of which accounted for 50% of summer ablation. This is consistent with field observations of subsurface streams and formation of a weathering crust. We identify an annual cycle of weathering crust formation in summer and its removal during the 10 months of winter sublimation

Changes in Functional Connectivity Following Treatment With Emotion Regulation Therapy

Emotion regulation therapy (ERT) is an efficacious treatment for distress disorders (i.e., depression and anxiety), predicated on a conceptual model wherein difficult to treat distress arises from intense emotionality (e.g., neuroticism, dispositional negativity) and is prolonged by negative self-referentiality (e.g., worry, rumination). Individuals with distress disorders exhibit disruptions in two corresponding brain networks including the salience network (SN) reflecting emotion/motivation and the default mode network (DMN) reflecting self-referentiality. Using resting-state functional connectivity (rsFC) analyses, seeded with primary regions in each of these networks, we investigated whether ERT was associated with theoretically consistent changes across nodes of these networks and whether these changes related to improvements in clinical outcomes. This study examined 21 generalized anxiety disorder (GAD) patients [with and without major depressive disorder (MDD)] drawn from a larger intervention trial (Renna et al., 2018a), who completed resting state fMRI scans before and after receiving 16 sessions of ERT. We utilized seed-based connectivity analysis with seeds in the posterior cingulate cortex (PCC), right anterior insula, and right posterior insula, to investigate whether ERT was associated with changes in connectivity of nodes of the DMN and SN networks to regions across the brain. Findings revealed statistically significant treatment linked changes in both the DMN and SN network nodes, and these changes were associated with clinical improvement corresponding to medium effect sizes. The results are discussed in light of a nuanced understanding of the role of connectivity changes in GAD and MDD, and begin to provide neural network support for the hypothesized treatment model predicated by ERT

Is there a causal relationship between acute stage sensorimotor cortex activity and the development of chronic low back pain? : a protocol and statistical analysis plan

Introduction: Why some people develop chronic pain following an acute episode of low back pain is unknown. Recent cross-sectional studies have suggested a relationship between aberrant sensorimotor cortex activity and pain persistence. The UPWaRD (Understanding persistent Pain Where it ResiDes) cohort study is the first prospective, longitudinal investigation of sensorimotor cortex activity in low back pain. This paper describes the development of a causal model and statistical analysis plan for investigating the causal effect of sensorimotor cortex activity on the development of chronic low back pain. Methods and analysis: Sensorimotor cortex activity was assessed within 6 weeks of low back pain onset using somatosensory evoked potentials and transcranial magnetic stimulation mapping techniques. Chronic low back pain is defined as ongoing pain (Numerical Rating score ≥1) or disability (Roland Morris Disability Questionnaire score ≥3) at 6 months follow-up. Variables that could confound the relationship between sensorimotor cortex activity and chronic low back pain were identified using a directed acyclic graph and content expertise was used to specify known causal paths. The statistical model was developed ‘a priori’ to control for confounding variables identified in the directed acyclic graph, allowing an unbiased estimate of the causal effect of sensorimotor activity in acute low back pain on the development of chronic pain. The statistical analysis plan was finalised prior to follow-up of all participants and initiation of analysis. Ethics and dissemination: Ethical approval has been obtained from Western Sydney University Human Research Ethics Committee (H10465) and from Neuroscience Research Australia (SSA: 16/002). Dissemination will occur through presentations at national and international conferences and publications in international peer-reviewed journals. Trial registration number: ACTRN12619000002189 (retrospectively registered)