The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages

Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNPs, generated via GBS, of southern bull-kelp (Durvillaea). Durvillaea chathamensis co-occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis, which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony-informative SNPs in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve.This research was supported by an Australian Research Council Discovery Early Career Research Award (DE140101715 to CIF) and University of Otago Performance Based Research Funding (to JMW)

Theory of high-energy emission from the pulsar/Be-star system PSR 1259−-63 I: radiation mechanisms and interaction geometry

We study the physical processes of the PSR B1259-63 system containing a 47 ms pulsar orbiting around a Be star in a highly eccentric orbit. Motivated by the results of a multiwavelength campaign during the January 1994 periastron passage of PSR B1259-63, we discuss several issues regarding the mechanism of high-energy emission. Unpulsed power law emission from the this system was detected near periastron in the energy range 1-200 keV. We find that the observed high energy emission from the PSR B1259-63 system is not compatible with accretion or propeller-powered emission. Shock-powered high-energy emission produced by the pulsar/outflow interaction is consistent with all high energy observations. By studying the evolution of the pulsar cavity we constrain the magnitude and geometry of the mass outflow outflow of the Be star. The pulsar/outflow interaction is most likely mediated by a collisionless shock at the internal boundary of the pulsar cavity. The system shows all the characteristics of a {\it binary plerion} being {\it diffuse} and {\it compact} near apastron and periastron, respectively. The PSR B1259-63 cavity is subject to different radiative regimes depending on whether synchrotron or inverse Compton (IC) cooling dominates the radiation of electron/positron pairs advected away from the inner boundary of the pulsar cavity. The highly non-thermal nature of the observed X-ray/gamma-ray emission near periastron establishes the existence of an efficient particle acceleration mechanism within a timescale shown to be less than $\sim 10^2-10^3$ s. A synchrotron/IC model of emission of e\pm-pairs accelerated at the inner shock front of the pulsar cavity and adiabatically expanding in the MHD flow provides an excellent explanation of the observed time variableX-ray flux and spectrum from the PSRComment: 68 pages, accepted for publication in the Astrophys. J. on Aug. 26, 199

Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp

<p>Abstract</p> <p>Background</p> <p>South America's western coastline, extending in a near-straight line across some 35 latitudinal degrees, presents an elegant setting for assessing both contemporary and historic influences on cladogenesis in the marine environment. Southern bull-kelp (<it>Durvillaea antarctica</it>) has a broad distribution along much of the Chilean coast. This species represents an ideal model taxon for studies of coastal marine connectivity and of palaeoclimatic effects, as it grows only on exposed rocky coasts and is absent from beaches and ice-affected shores. We expected that, along the central Chilean coast, <it>D. antarctica </it>would show considerable phylogeographic structure as a consequence of the isolating effects of distance and habitat discontinuities. In contrast, we hypothesised that further south - throughout the region affected by the Patagonian Ice Sheet at the Last Glacial Maximum (LGM) - <it>D. antarctica </it>would show relatively little genetic structure, reflecting postglacial recolonisation.</p> <p>Results</p> <p>Mitochondrial (COI) and chloroplast (<it>rbc</it>L) DNA analyses of <it>D. antarctica </it>from 24 Chilean localities (164 individuals) revealed two deeply divergent (4.5 - 6.1% for COI, 1.4% for <it>rbc</it>L) clades from the centre and south of the country, with contrasting levels and patterns of genetic structure. Among populations from central Chile (32° - 44°S), substantial phylogeographic structure was evident across small spatial scales, and a significant isolation-by-distance effect was observed. Genetic disjunctions in this region appear to correspond to the presence of long beaches. In contrast to the genetic structure found among central Chilean populations, samples from the southern Chilean Patagonian region (49° - 56°S) were genetically homogeneous and identical to a haplotype recently found throughout the subantarctic region.</p> <p>Conclusions</p> <p>Southern (Patagonian) Chile has been recolonised by <it>D. antarctica </it>relatively recently, probably since the LGM. The inferred trans-oceanic ancestry of these Patagonian populations supports the notion that <it>D. antarctica </it>is capable of long-distance dispersal via rafting. In contrast, further north in central Chile, the correspondence of genetic disjunctions in <it>D. antarctica </it>with long beaches indicates that habitat discontinuity drives genetic isolation among established kelp populations. We conclude that rafting facilitates colonisation of unoccupied shores, but has limited potential to enhance gene-flow among established populations. Broadly, this study demonstrates that some taxa may be considered to have either high or low dispersal potential across different temporal and geographic scales.</p

The effect of weak inertia in rotating high-aspect-ratio vessel bioreactors

One method to grow artificial body tissue is to place a porous scaffold seeded with cells, known as a tissue construct, into a rotating bioreactor filled with a nutrient-rich fluid. The flow within the bioreactor is affected by the movement of the construct relative to the bioreactor which, in turn, is affected by the hydrodynamical and gravitational forces the construct experiences. The construct motion is thus coupled to the flow within the bioreactor. Over the timescale of a few hours, the construct appears to move in a periodic orbit but, over tens of hours, the construct drifts from periodicity. In the biological literature, this effect is often attributed to the change in density of the construct that occurs via tissue growth. In this paper, we show that weak inertia can cause the construct to drift from its periodic orbit over the same timescale as tissue growth. We consider the coupled flow and construct motion problem within a rotating high-aspect- ratio vessel bioreactor. Using an asymptotic analysis, we investigate the case where the Reynolds number is large but the geometry of the bioreactor yields a small reduced Reynolds number, resulting in a weak inertial effect. In particular, to accurately couple the bioreactor and porous flow regions, we extend the nested boundary layer analysis of Dalwadi et al. (J. Fluid Mech. vol. 798, pp. 88–139, 2016) to include moving walls and the thin region between the porous construct and the bioreactor wall. This allows us to derive a closed system of nonlinear ordinary differential equations for the construct trajectory, from which we show that neglecting inertia results in periodic orbits; we solve the inertia-free problem analytically, calculating the periodic orbits in terms of the system parameters. Using a multiple-scale analysis, we then systematically derive a simpler system of nonlinear ordinary differential equations that describe the long-time drift of the construct due to the effect of weak inertia. We investigate the bifurcations of the construct trajectory behaviour, and the limit cycles that appear when the construct is less dense than the surrounding fluid and the rotation rate is large enough. Thus, we are able to predict when the tissue construct will drift towards a stable limit cycle within the bioreactor and when it will drift out until it hits the bioreactor edg

Genetic affinities between trans-oceanic populations of non-buoyant macroalgae in the high latitudes of the Southern Hemisphere

Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships - even shared haplotypes - were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.This work was funded by New Zealand Marsden contract 07-UOO-099, Department of Zoology and University of Otago Research grants to JMW and CIF; a Shackleton Scholarship to CIF; an Allan Wilson Centre for Molecular Ecology and Evolution postdoctoral grant to CIF; Australian Antarctic Division AAS project #2914

On the boundary layer structure near a highly permeable porous interface

The method of matched asymptotic expansions is used to study the canonical problem of steady laminar flow through a narrow two-dimensional channel blocked by a tight-fitting finite-length highly permeable porous obstacle. We investigate the behaviour of the local flow close to the interface between the single-phase and porous regions (governed by the incompressible Navier--Stokes and Darcy flow equations, respectively). We solve for the flow in these inner regions in the limits of low and high Reynolds number, facilitating an understanding of the nature of the transition from Poiseuille to plug to Poiseuille flow in each of these limits. Significant analytical progress is made in the high-Reynolds-number limit, and we explore in detail the rich boundary layer structure that occurs. We derive general results for the interfacial stress and for the conditions that couple the flow in the outer regions away from the interface. We consider the three-dimensional generalization to unsteady laminar flow through and around a tight-fitting highly permeable cylindrical porous obstacle within a Hele-Shaw cell. For the high-Reynolds-number limit, we give the coupling conditions and interfacial stress in terms of the outer flow variables, allowing information from a nonlinear three-dimensional problem to be obtained by solving a linear two-dimensional problem. Finally, we illustrate the utility of our analysis by considering the specific example of time-dependent forced far-field flow in a Hele-Shaw cell containing a porous cylinder with a circular cross-section. We determine the internal stress within the porous obstacle, which is key for tissue engineering applications, and the interfacial stress on the boundary of the porous obstacle, which has applications to biofilm erosion. In the high-Reynolds-number limit, we demonstrate that the fluid inertia can result in the cylinder experiencing a time-independent net force, even when the far-field forcing is periodic with zero mean

UV Shielding of Bacillus pumilus SAFR-032 Endospores by Martian Regolith Simulants

As exploration of the solar system advances with life detection missions on the horizon, the concern for planetary protection has grown considerably. When attempting to detect extraterrestrial life, the likelihood of false positives from terrestrial contamination must be minimized. The Exposing Microorganisms in the Stratosphere (E-MIST) balloon project aims to evaluate whether resilient terrestrial bacteria can survive stressors in a Mars-like environment. This is accomplished by sending Bacillus pumilus SAFR-032, an endospore-forming bacterial isolate from a spacecraft assembly facility, to the Earth's middle stratosphere (30-38 kilometers), where low temperature and pressure and high radiation and dryness conditions are similar to the surface of Mars. Previous ground and flight tests showed that the vast majority of SAFR-032 spores (99.99 percent) were inactivated by direct sunlight due to ultraviolet (UV) radiation. This observation led us to explore the role of dust shielding in changing microbial survivorship outcomes. To determine the dust particle distributions and density for potentially shielding microbes from UV radiation, samples of a Martian dust simulant were mixed with SAFR-032 spores. The dry heat sterilized simulant used was JSC MARS-1, weathered volcanic ash from Hawaii that displays many chemical and physical properties similar to the Martian soil as characterized by the Viking Lander 1, including reflectance spectrum, chemical composition, mineralogy, grain size, specific gravity, and magnetic properties. First, scanning electron microscopy was undertaken to visualize the aggregation of the spores with dust particles (i.e., shading effects), and samples of varying dust concentrations were subsequently irradiated with UVC light to test survivorship outcomes. After a relationship between dust concentration and spore survivorship was determined, a solar simulator capable of irradiating samples with a fuller UV spectrum (less than 280-400 nanometers) was used to perform a more robust middle stratosphere simulation. Taken together, we will use results from the ground-based irradiation studies to feed into experimental designs for the next E-MIST ultra-long duration polar balloon flight launched by NASA

The genomic footprint of coastal earthquake uplift

Theory suggests that catastrophic earth-history events can drive rapid biological evolution, but empirical evidence for such processes is scarce. Destructive geological events such as earthquakes can represent large-scale natural experiments for inferring such evolutionary processes. We capitalized on a major prehistoric (800 yr BP) geological uplift event affecting a southern New Zealand coastline to test for the lasting genomic impacts of disturbance. Genome-wide analyses of three co-distributed keystone kelp taxa revealed that post-earthquake recolonization drove the evolution of novel, large-scale intertidal spatial genetic ‘sectors’ which are tightly linked to geological fault boundaries. Demographic simulations confirmed that, following widespread extirpation, parallel expansions into newly vacant habitats rapidly restructured genome-wide diversity. Interspecific differences in recolonization mode and tempo reflect differing ecological constraints relating to habitat choice and dispersal capacity among taxa. This study highlights the rapid and enduring evolutionary effects of catastrophic ecosystem disturbance and reveals the key role of range expansion in reshaping spatial genetic patterns

Anon-Pass: Practical Anonymous Subscriptions

We present the design, security proof, and implementation of an anonymous subscription service. Users register for the service by providing some form of identity, which might or might not be linked to a real-world identity such as a credit card, a web login, or a public key. A user logs on to the system by presenting a credential derived from information received at registration. Each credential allows only a single login in any authentication window, or epoch. Logins are anonymous in the sense that the service cannot distinguish which user is logging in any better than random guessing. This implies unlinkability of a user across different logins. We find that a central tension in an anonymous subscription service is the service provider’s desire for a long epoch (to reduce server-side computation) versus users’ desire for a short epoch (so they can repeatedly “re-anonymize” their sessions). We balance this tension by having short epochs, but adding an efficient operation for clients who do not need unlinkability to cheaply re-authenticate themselves for the next time period. We measure performance of a research prototype of our pro- tocol that allows an independent service to offer anonymous access to existing services. We implement a music service, an Android-based subway-pass application, and a web proxy, and show that adding anonymity adds minimal client latency and only requires 33 KB of server memory per active user

Mathematical modelling of cell layer growth in a hollow fibre bioreactor.

Generating autologous tissue grafts of a clinically useful volume requires efficient and controlled expansion of cell populations harvested from patients. Hollow fibre bioreactors show promise as cell expansion devices, owing to their potential for scale-up. However, further research is required to establish how to specify appropriate hollow fibre bioreactor operating conditions for expanding different cell types. In this study we develop a simple model for the growth of a cell layer seeded on the outer surface of a single fibre in a perfused hollow fibre bioreactor. Nutrient-rich culture medium is pumped through the fibre lumen and leaves the bioreactor via the lumen outlet or passes through the porous fibre walls and cell layer, and out via ports on the outer wall of the extra-capillary space. Stokes and Darcy equations for fluid flow in the fibre lumen, fibre wall, cell layer and extra-capillary space are coupled to reaction-advection-diffusion equations for oxygen and lactate transport through the bioreactor, and to a simple growth law for the evolution of the free boundary of the cell layer. Cells at the free boundary are assumed to proliferate at a rate that increases with the local oxygen concentration, and to die and detach from the layer if the local fluid shear stress or lactate concentration exceed critical thresholds. We use the model to predict operating conditions that maximise the cell layer growth for different cell types. In particular, we predict the optimal flow rate of culture medium into the fibre lumen and fluid pressure imposed at the lumen outlet for cell types with different oxygen demands and fluid shear stress tolerances, and compare the growth of the cell layer when the exit ports on the outside of the bioreactor are open with that when they are closed. Model simulations reveal that increasing the inlet flow rate and outlet fluid pressure increases oxygen delivery to the cell layer and, therefore, the growth rate of cells that are tolerant to high shear stresses, but may be detrimental for shear-sensitive cells. The cell layer growth rate is predicted to increase, and be less sensitive to the lactate tolerance of the cells, when the exit ports are opened, as the radial flow through the bioreactor is enhanced and the lactate produced by the cells cleared more rapidly from the cell layer