Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many ...existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.
This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package.
mwpennell@gmail.com
Supplementary data are available at Bioinformatics online.
•Protocol-based resuscitation is critical to successfully manage these potentially severely injured patients in a well-coordinated manner.•The first step of resuscitation bay should be the immediate ...application of a circumferential pelvic sheet or binder, initiation of 1:1:1 pRBC:FFP:platelets or whole blood, and to•TXA should be considered as a safe adjunct to treat coagulopathy.•Percutaneous selective angiography has been shown to be efficacious for patients with clinical indicators of arterial injury.•For patients in extremis, REBOA should be considered to allow continued appropriate resuscitation while limiting further hemorrhage.
Patients with a pelvic ring injury and hemodynamic instability can be challenging to manage with high rates of morbidity and mortality rates. Protocol-based resuscitation strategies are critical to successfully manage these potentially severely injured patients in a well-coordinated manner. While some aspects of treatment may vary slightly from institution to institution, it is critical to identify pelvic injuries and their associated injuries expediently. The first step at the scene of injury or in the trauma resuscitation bay should be the immediate application of a circumferential pelvic sheet or binder, initiation of physiologically optimal fluid resuscitation in the form 1:1:1 (pRBC:FFP:platelets) or whole blood, and to consider TXA as a safe adjunct to treat coagulopathy. Providers should have a very low threshold for emergent operative intervention in the form of pelvic external fixation and/or pelvic packing. This occurs in addition to simultaneous interventions addressing the other possible sources of bleeding in patients demonstrating signs of hemorrhagic shock and failure to respond to early resuscitation and external pelvic tamponade. Finally, while arterial injury is only present in a small percentage of patients with a pelvic ring injury, percutaneous vascular intervention with selective angiography and REBOA have been shown to be efficacious for patients with clinical indicators of arterial injury or who remain hemodynamically unstable despite external pelvic tamponade and packing to address venous bleeding. They should be performed when as early as possible for patients in true extremis limit further hemorrhage and allow resuscitation efforts to continue.
Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity.
Using a time-calibrated phylogeny, we characterized hot and cold ...spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events.
Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of ‘nested radiations’ – increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model.
Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period.
Evolutionary biologists since Darwin have been fascinated by differences in the rate of trait-evolutionary change across lineages. Despite this continued interest, we still lack methods for ...identifying shifts in evolutionary rates on the growing tree of life while accommodating uncertainty in the evolutionary process. Here we introduce a Bayesian approach for identifying complex patterns in the evolution of continuous traits. The method (auteur) uses reversible-jump Markov chain Monte Carlo sampling to more fully characterize the complexity of trait evolution, considering models that range in complexity from those with a single global rate to potentially ones in which each branch in the tree has its own independent rate. This newly introduced approach performs well in recovering simulated rate shifts and simulated rates for datasets nearing the size typical for comparative phylogenetic study (i.e., ≥ 64 tips). Analysis of two large empirical datasets of vertebrate body size reveal overwhelming support for multiple-rate models of evolution, and we observe exceptionally high rates of body-size evolution in a group of emydid turtles relative to their evolutionary background, auteur will facilitate identification of exceptional evolutionary dynamics, essential to the study of both adaptive radiation and stasis.
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium ...proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales.
Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread ...and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.
Understanding the evolutionary history of microbial pathogens is critical for mitigating the impacts of emerging infectious diseases on economically and ecologically important host species. We used a ...genome resequencing approach to resolve the evolutionary history of an important microbial pathogen, the chytrid Batrachochytrium dendrobatidis (Bd), which has been implicated in amphibian declines worldwide. We sequenced the genomes of 29 isolates of Bd from around the world, with an emphasis on North, Central, and South America because of the devastating effect that Bd has had on amphibian populations in the New World. We found a substantial amount of evolutionary complexity in Bd with deep phylogenetic diversity that predates observed global amphibian declines. By investigating the entire genome, we found that even the most recently evolved Bd clade (termed the global panzootic lineage) contained more genetic variation than previously reported. We also found dramatic differences among isolates and among genomic regions in chromosomal copy number and patterns of heterozygosity, suggesting complex and heterogeneous genome dynamics. Finally, we report evidence for selection acting on the Bd genome, supporting the hypothesis that protease genes are important in evolutionary transitions in this group. Bd is considered an emerging pathogen because of its recent effects on amphibians, but our data indicate that it has a complex evolutionary history that predates recent disease outbreaks. Therefore, it is important to consider the contemporary effects of Bd in a broader evolutionary context and identify specific mechanisms that may have led to shifts in virulence in this system.
•The purpose of this study is to provide an analysis of iliosacral screw insertion sites on the posterior ilium.•Improved outcomes of LC II injuries treated percutaneously marks the importance of a ...preoperative plan to determine amenability of percutaneous iliosacral screw fixation.•Mapping iliosacral screw start sites can be helpful for preoperative planning of percutaneous pelvic ring injury fixation.•This has demonstrated a relatively predictable region of screw start site on the posterior ilium, which is dependent on the sacral morphology and sacral level.•Iliosacral screws start sites on the posterior ilium have reliable regions that can be used to plan posterior fixation of pelvic ring injuries.
Lateral compression type II pelvic ring injuries can be treated with fixation through open or percutaneous approaches depending on the injury pattern and available osseous fixation pathways. The start site of iliosacral screws to stabilize these injuries should be on the unstable posterior iliac fragment; however, our understanding of start sites for iliosacral screws has not been developed. The purpose of this study is to provide an analysis of iliosacral screw start sites on the posterior ilium to help guide treatment of pelvic ring injuries.
One-hundred and seventeen consecutive patients at an academic level I trauma center with pelvic ring injuries who underwent surgical treatment with iliosacral screws were included in the final analysis. The start sites of iliosacral screws with confirmed intraosseous placement on a postoperative computed tomography were mapped on the posterior ilium and analyzed according to the sacral segment and type of iliosacral screw.
One-hundred and seventeen patients were included in the final analysis. Of the total of 272 iliosacral screw insertion sites analyzed, 145 (53%) were sacroiliac-style screws and 127 (47%) were transsacral screws. The insertion sites for sacroiliac-style screws and transsacral screws at different sacral segment levels can vary but have predictable regions on the posterior ilium relative to reliable osseous landmarks.
Iliosacral screws start sites on the posterior ilium have reliable regions that can be used to plan posterior fixation of pelvic ring injuries.
Spinopelvic dissociation injuries are complex injuries defined as discontinuity between the appendicular and axial skeleton. Fracture patterns are variable, but U-type and H-type fractures are common ...and often present with kyphotic deformity along with translational displacement and impaction. The ideal method of fixation has not been established for these injuries. The goals of treatment include restoration of alignment, stability, and neural decompression as needed. Traditional methods of lumbopelvic fixation have spanned the upper sacral fracture site. Our novel modified method of lumbopelvic fixation directly instruments the S1 body. This allows for direct manipulation of the fracture which we theorize improves reduction and increases stability across the fracture. This article characterizes the injury patterns, outlines the modified technique, and reports the clinical and radiographic outcomes of our modified lumbopelvic fixation technique and construct.
Multidimensional fluoroscopy has been increasingly used in orthopaedic trauma to improve the intraoperative assessment of articular reductions and implant placement. Owing to the complex osteology of ...the pelvis, cross-sectional imaging is imperative for accurate evaluation of pelvic ring and acetabular injuries both preoperatively and intraoperatively. The continued development of fluoroscopic technology over the past decade has resulted in improved ease of intraoperative multidimensional fluoroscopy use in pelvic and acetabular surgery. This has provided orthopaedic trauma surgeons with a valuable tool to better evaluate reduction and fixation at different stages during operative treatment of these injuries. Specifically, intraoperative 3D fluoroscopy during treatment of acetabulum and pelvis injuries assists with guiding intraoperative decisions, assessing reductions, ensuring implant safety, and confirming appropriate fixation. We outline the useful aspects of this technology during pelvic and acetabular surgery and report its utility with a consecutive case series at a single institution. The added benefits of this technology have improved the ability to effectively manage patients with pelvis and acetabulum injuries.
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