The impact of rate heterogeneity on inference of phylogenetic models of trait evolution

Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small-scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate-static and variable-rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate-heterogeneity scenarios. Our results show that rate heterogeneity is present across small-scaled avian clades, and consequently applying only standard single-process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable-rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable-rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit

Extensional rheology and elastic instabilities of a wormlike micellar solution in a microfluidic cross-slot device

Wormlike micellar surfactant solutions are encountered in a wide variety of important applications, including enhanced oil recovery and ink-jet printing, in which the fluids are subjected to high extensional strain rates. In this contribution we present an experimental investigation of the flow of a model wormlike micellar solution (cetyl pyridinium chloride and sodium salicylate in deionised water) in a well-defined stagnation point extensional flow field generated within a microfluidic cross-slot device. We use micro-particle image velocimetry (m-PIV) and full-field birefringence microscopy coupled with macroscopic measurements of the bulk pressure drop to make a quantitative characterization of the fluid’s rheological response over a wide range of deformation rates. The flow field in the micromachined cross-slot is first characterized for viscous flow of a Newtonian fluid, and m-PIV measurements show the flow field remains symmetric and stable up to moderately high Reynolds number, Re z 20, and nominal strain rate, _3nom z 635 s1. By contrast, in the viscoelastic micellar solution the flow field remains symmetric only for low values of the strain rate such that _3nom # lM1, where lM ¼ 2.5 s is the Maxwell relaxation time of the fluid. In this stable flow regime the fluid displays a localized and elongated birefringent strand extending along the outflow streamline from the stagnation point, and estimates of the apparent extensional viscosity can be obtained using the stressoptical rule and from the total pressure drop measured across the cross-slot channel. For moderate deformation rates (_3nom $ lM1) the flow remains steady, but becomes increasingly asymmetric with increasing flow rate, eventually achieving a steady state of complete anti-symmetry characterized by a dividing streamline and birefringent strand connecting diagonally opposite corners of the cross-slot. Eventually, as the nominal imposed deformation rate is increased further, the asymmetric divided flow becomes time dependent. These purely elastic instabilities are reminiscent of those observed in crossslot flows of polymer solutions, but seem to be strongly influenced by the effects of shear localization of the micellar fluid within the microchannels and around the re-entrant corners of the cross-slot

On the existence of finite-energy lumps in classic field theories

We show how the existence of non-trivial finite-energy time-dependent classical lumps is restricted by a generalized virial theorem. For simple model Lagrangians, bounds on energies follow.Comment: 4 pages, 1 figure; substantial change

Dating placentalia: Morphological clocks fail to close the molecular fossil gap

Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crowngroup placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip-calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, 130–145 million years ago (Ma), than fossil and molecular clock data (80–90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected. We recommend that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution

Trait Evolution in Adaptive Radiations: Modeling and Measuring Interspecific Competition on Phylogenies

The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species. Competition is modeled as a tendency of sympatric species to evolve toward difference from one another, producing trait overdispersion and high phylogenetic signal. The model predicts elevated trait variance across species and a slowdown in evolutionary rate both across the clade and within each branch. The model also predicts a reduction in correlation between otherwise correlated traits. We use an approximate Bayesian computation approach to estimate model parameters. We find reasonable power to detect competition in sufficiently large (20+ species) trees compared with Brownian trait evolution and with Ornstein-Uhlenbeck and early burst models. We apply the model to examine the evolution of bill morphology of Darwin’s finches and find evidence that competition affects the evolution of bill length

Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae

Extracytoplasmic solute receptors (ESRs) are important components of solute uptake systems in bacteria, having been studied extensively as parts of ATP binding cassette transporters. Herein we report the first crystal structure of an ESR protein from a functionally characterized electrochemical ion gradient-dependent secondary transporter. This protein, SiaP, forms part of a tripartite ATP-independent periplasmic transporter specific for sialic acid in Haemophilus influenzae. Surprisingly, the structure reveals an overall topology similar to ATP binding cassette ESR proteins, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component. The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxyN-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics as determined by stopped-flow fluorescence spectroscopy, is accompanied by domain closure about a hinge region and the kinking of an alpha-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of ESR-dependent secondary transporters that are widespread in prokaryotes

Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity

The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. All catabolic pathways must begin with the transport of substrate from the environment through the cytoplasmic membrane, a role executed by membrane transporters. Although several classes of cytoplasmic membrane transporters are described, high-affinity uptake of substrates occurs through Solute Binding-Protein (SBP) dependent systems. Three families of SBP dependant transporters are known; the primary ATP-binding cassette (ABC) transporters, and the secondary Tripartite ATP-independent periplasmic (TRAP) transporters and Tripartite Tricarboxylate Transporters (TTT). Far less well understood than the ABC family, the TRAP transporters are found to be abundant among bacteria from marine environments, and the TTT transporters are the most abundant family of proteins in many species of β-proteobacteria. In this review, recent knowledge about these families is covered, with emphasis on their physiological and structural mechanisms, relating to several examples of relevant uptake systems in pathogenicity and colonization, using the SiaPQM sialic acid uptake system from Haemophilus influenzae and the TctCBA citrate uptake system of Salmonella typhimurium as the prototypes for the TRAP and TTT transporters, respectively. High-throughput analysis of SBPs has recently expanded considerably the range of putative substrates known for TRAP transporters, while the repertoire for the TTT family has yet to be fully explored but both types of systems most commonly transport carboxylates. Specialized spectroscopic techniques and site-directed mutagenesis have enriched our knowledge of the way TRAP binding proteins capture their substrate, while structural comparisons show conserved regions for substrate coordination in both families. Genomic and protein sequence analyses show TTT SBP genes are strikingly overrepresented in some bacteria, especially in the β-proteobacteria and some α-proteobacteria. The reasons for this are not clear but might be related to a role for these proteins in signaling rather than transport

Polarized Protons in HERA

Polarized proton beams at HERA can currently only be produced by extracting a beam from a polarized source and then accelerating it in the three synchrotrons at DESY. In this paper, the processes which can depolarize a proton beam in circular accelerators are explained, devices which could avoid this depolarization in the DESY accelerator chain are described, and specific problems which become important at the high energies of HERA are mentioned. At HERA's high energies, spin motion cannot be accurately described with the isolated resonance model which has been successfully used for lower energy rings. To illustrate the principles of more accurate simulations, the invariant spin field is introduced to describe the equilibrium polarization state of a beam and the changes during acceleration. It will be shown how linearized spin motion leads to a computationally quick approximation for the invariant spin field and how to amend this with more time consuming but accurate non-perturbative computations. Analysis with these techniques has allowed us to establish optimal Siberian Snake schemes for HERA