Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

K.L. was funded by a junior research fellowship from the National Environmental Research Council, UK (NE/I020288/1, NBAF659).Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here, we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced postdivergence gene flow that ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of species divergence which is compatible with theoretical models that posit a role of inversions in speciation with gene flow.Publisher PDFPeer reviewe

Non-Oberbeck-Boussinesq effects in two-dimensional Rayleigh-Benard convection in glycerol

We numerically analyze Non-Oberbeck-Boussinesq (NOB) effects in two-dimensional Rayleigh-Benard flow in glycerol, which shows a dramatic change in the viscosity with temperature. The results are presented both as functions of the Rayleigh number (Ra) up to $10^8$ (for fixed temperature difference between the top and bottom plates) and as functions of "non-Oberbeck-Boussinesqness'' or "NOBness'' ($\Delta$) up to 50 K (for fixed Ra). For this large NOBness the center temperature $T_c$ is more than 5 K larger than the arithmetic mean temperature $T_m$ between top and bottom plate and only weakly depends on Ra. To physically account for the NOB deviations of the Nusselt numbers from its Oberbeck-Boussinesq values, we apply the decomposition of $Nu_{NOB}/Nu_{OB}$ into the product of two effects, namely first the change in the sum of the top and bottom thermal BL thicknesses, and second the shift of the center temperature $T_c$ as compared to $T_m$. While for water the origin of the $Nu$ deviation is totally dominated by the second effect (cf. Ahlers et al., J. Fluid Mech. 569, pp. 409 (2006)) for glycerol the first effect is dominating, in spite of the large increase of $T_c$ as compared to $T_m$.Comment: 6 pages, 7 figure

Response maxima in time-modulated turbulence: Direct Numerical Simulations

The response of turbulent flow to time-modulated forcing is studied by direct numerical simulations of the Navier-Stokes equations. The large-scale forcing is modulated via periodic energy input variations at frequency $\omega$. The response is maximal for frequencies in the range of the inverse of the large eddy turnover time, confirming the mean-field predictions of von der Heydt, Grossmann and Lohse (Phys. Rev. E 67, 046308 (2003)). In accordance with the theory the response maximum shows only a small dependence on the Reynolds number and is also quite insensitive to the particular flow-quantity that is monitored, e.g., kinetic energy, dissipation-rate, or Taylor-Reynolds number. At sufficiently high frequencies the amplitude of the kinetic energy response decreases as $1/\omega$. For frequencies beyond the range of maximal response, a significant change in phase-shift relative to the time-modulated forcing is observed.Comment: submitted to Europhysics Letters (EPL), 8 pages, 8 Postscript figures, uses epl.cl

Periodically driven Taylor-Couette turbulence

We study periodically driven Taylor-Couette turbulence, i.e. the flow confined between two concentric, independently rotating cylinders. Here, the inner cylinder is driven sinusoidally while the outer cylinder is kept at rest (time-averaged Reynolds number is $Re_i = 5 \times 10^5$). Using particle image velocimetry (PIV), we measure the velocity over a wide range of modulation periods, corresponding to a change in Womersley number in the range $15 \leq Wo \leq 114$. To understand how the flow responds to a given modulation, we calculate the phase delay and amplitude response of the azimuthal velocity. In agreement with earlier theoretical and numerical work, we find that for large modulation periods the system follows the given modulation of the driving, i.e. the system behaves quasi-stationary. For smaller modulation periods, the flow cannot follow the modulation, and the flow velocity responds with a phase delay and a smaller amplitude response to the given modulation. If we compare our results with numerical and theoretical results for the laminar case, we find that the scalings of the phase delay and the amplitude response are similar. However, the local response in the bulk of the flow is independent of the distance to the modulated boundary. Apparently, the turbulent mixing is strong enough to prevent the flow from having radius-dependent responses to the given modulation.Comment: 12 pages, 6 figure

Clinical and functional characterisation of a novel TNFRSF1A c.605T > A/V173D cleavage site mutation associated with tumour necrosis factor receptor-associated periodic fever syndrome (TRAPS), cardiovascular complications and excellent response to etanercept treatment.

Objectives: To study the clinical outcome, treatment response, T-cell subsets and functional consequences of a novel tumour necrosis factor (TNF) receptor type 1 (TNFRSF1A) mutation affecting the receptor cleavage site. Methods: Patients with symptoms suggestive of tumour necrosis factor receptor-associated periodic syndrome (TRAPS) and 22 healthy controls (HC) were screened for mutations in the TNFRSF1A gene. Soluble TNFRSF1A and inflammatory cytokines were measured by ELISAs. TNFRSF1A shedding was examined by stimulation of peripheral blood mononuclear cells (PBMCs) with phorbol 12-myristate 13-acetate followed by flow cytometric analysis (FACS). Apoptosis of PBMCs was studied by stimulation with TNFa in the presence of cycloheximide and annexin V staining. T cell phenotypes were monitored by FACS. Results: TNFRSF1A sequencing disclosed a novel V173D/ p.Val202Asp substitution encoded by exon 6 in one family, the c.194–14G.A splice variant in another and the R92Q/p.Arg121Gln substitution in two families. Cardiovascular complications (lethal heart attack and peripheral arterial thrombosis) developed in two V173D patients. Subsequent etanercept treatment of the V173D carriers was highly effective over an 18-month follow-up period. Serum TNFRSF1A levels did not differ between TRAPS patients and HC, while TNFRSF1A cleavage from monocytes was significantly reduced in V173D and R92Q patients. TNFa-induced apoptosis of PBMCs and T-cell senescence were comparable between V173D patients and HC. Conclusions: The TNFRSF1A V173D cleavage site mutation may be associated with an increased risk for cardiovascular complications and shows a strong response to etanercept. T-cell senescence does not seem to have a pathogenetic role in affected patients

Concurrent TNFRSF1A R92Q and pyrin E230K mutations in a child with multiple sclerosis

We report a 16-year-old female patient with a severe course of multiple sclerosis and concomitant symptoms suggestive of a hereditary autoinflammatory disease. Genetic analyses revealed that she inherited a TNFRSF1A R92Q mutation from her mother and a pyrin E230K mutation from her father. To our knowledge, this is the first report of a patient with severe childhood multiple sclerosis and mutations in two genes which predispose to hereditary autoinflammatory disorders. We speculate that these mutations contribute to early multiple sclerosis manifestation and enhance the inflammatory damage inflicted by the autoimmune response

Hysteretic clustering in granular gas

Granular material is vibro-fluidized in N=2 and N=3 connected compartments, respectively. For sufficiently strong shaking the granular gas is equi-partitioned, but if the shaking intensity is lowered, the gas clusters in one compartment. The phase transition towards the clustered state is of 2nd order for N=2 and of 1st order for N=3. In particular, the latter is hysteretic. The experimental findings are accounted for within a dynamical model that exactly has the above properties

Archeological Survey Investigations at Martin Creek Lake State Park, Rusk County, Texas

An intensive cultural resources survey was conducted at Martin Creek Lake State Park by the Center for Archaeological Studies and Archeological & Environmental Consultants, LLC in June 2010 under contract with Texas Parks and Wildlife Department. Although previous investigations had been carried out in the park, no comprehensive survey had been completed that would allow TPWD and park management personnel to appropriately manage the park’s cultural resources in accordance with state law. During the 2010 survey, the park was stratified into areas with high, medium, and low probability of containing archaeological sites. A total of 423 shovel tests were excavated in these areas; four new sites were documented and nine previously reported sites were revisited and assessed. These 13 sites reflect historic era occupations in the park dating from the mid-1800s to the mid-1900s and prehistoric occupations that include Late Archaic, Woodland, and Caddo components

Heat transfer mechanisms in bubbly Rayleigh-Benard convection

The heat transfer mechanism in Rayleigh-Benard convection in a liquid with a mean temperature close to its boiling point is studied through numerical simulations with point-like vapor bubbles, which are allowed to grow or shrink through evaporation and condensation and which act back on the flow both thermally and mechanically. It is shown that the effect of the bubbles is strongly dependent on the ratio of the sensible heat to the latent heat as embodied in the Jacob number Ja. For very small Ja the bubbles stabilize the flow by absorbing heat in the warmer regions and releasing it in the colder regions. With an increase in Ja, the added buoyancy due to the bubble growth destabilizes the flow with respect to single-phase convection and considerably increases the Nusselt number.Comment: 11 pages, 14 figure