A molecular timescale of eukaryote evolution and the rise of complex multicellular life

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10 types at 1500 Ma and 50 cell types at ~1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2–3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity

Production of a Prompt Photon in Association with Charm at Next-to-Leading Order in QCD

A second order, $O(\alpha ^2_s)$, calculation in perturbative quantum chromodynamics of the two particle inclusive cross section is presented for the reaction $p +\bar{p}\rightarrow \gamma + c + X$ for large values of the transverse momentum of the prompt photon and charm quark. The combination of analytic and Monte Carlo integration methods used here to perform phase-space integrations facilitates imposition of photon isolation restrictions and other selections of relevance in experiments. Differential distributions are provided for various observables. Positive correlations in rapidity are predicted.Comment: 27 pages in RevTex plus 14 figures in one compressed PS fil

On transversally elliptic operators and the quantization of manifolds with ff-structure

An $f$-structure on a manifold $M$ is an endomorphism field \phi\in\Gamma(M,\End(TM)) such that $\phi^3+\phi=0$. Any $f$-structure $\phi$ determines an almost CR structure E_{1,0}\subset T_\C M given by the $+i$-eigenbundle of $\phi$. Using a compatible metric $g$ and connection $\nabla$ on $M$, we construct an odd first-order differential operator $D$, acting on sections of $\S=\Lambda E_{0,1}^*$, whose principal symbol is of the type considered in arXiv:0810.0338. In the special case of a CR-integrable almost $\S$-structure, we show that when $\nabla$ is the generalized Tanaka-Webster connection of Lotta and Pastore, the operator $D$ is given by D = \sqrt{2}(\dbbar+\dbbar^*), where \dbbar is the tangential Cauchy-Riemann operator. We then describe two "quantizations" of manifolds with $f$-structure that reduce to familiar methods in symplectic geometry in the case that $\phi$ is a compatible almost complex structure, and to the contact quantization defined in \cite{F4} when $\phi$ comes from a contact metric structure. The first is an index-theoretic approach involving the operator $D$; for certain group actions $D$ will be transversally elliptic, and using the results in arXiv:0810.0338, we can give a Riemann-Roch type formula for its index. The second approach uses an analogue of the polarized sections of a prequantum line bundle, with a CR structure playing the role of a complex polarization.Comment: 31 page

Bioturbation and particle transport in Carolina slope sediments: A radiochemical approach

In situ tracer experiments investigated short-term sediment mixing processes at two Carolina continental margin sites (water depth = 850 m) characterized by different organic C fluxes, 234Th mixing coefficients (Db) and benthic assemblages. Phytoplankton, slope sediment, and sand-sized glass beads tagged with 210Pb, 113Sn, and 228Th, respectively, were placed via submersible at the sediment-water interface at both field sites (Site I off Cape Fear, and Site III off Cape Hatteras). Experimental plots were sampled at 0, 1.5 days, and 90 days after tracer emplacement to examine short-term, vertical transport. Both sites are initially dominated by nonlocal mixing. Transport to the bottom of the surface mixed layer at both sites occurs more rapidly than 234Th-based Db values predict; after 1.5 days, tagged particles were observed 5 cm below the sediment-water interface at Site I and 12 cm below at Site III. Impulse tracer profiles after 90 days at Site III exhibit primarily diffusive distributions, most likely due to a large number of random, nonlocal mixing events. The Db values determined from 90-day particle tagging experiments are comparable to those obtained from naturally occurring 234Th profiles (~100-day time scales) from nearby locations. The agreement between impulse tracer mixing coefficients and steady-state natural tracer mixing coefficients suggests that the diffusive analogue for bioturbation on monthly time scales is a realistic and useful approach. Tracer profiles from both sites exhibit some degree of particle selective mixing, but the preferential transport of the more labile carbon containing particles only occurred 30% of the time. Consequently, variations in the extent to which age-dependent mixing occurs in marine sediments may depend on factors such as faunal assemblage and organic carbon flux

The pre-shock gas of SN1006 from HST/ACS observations

We derive the pre-shock density and scale length along the line of sight for the collisionless shock from a deep HST image that resolves the H alpha filament in SN1006 and updated model calculations. The very deep ACS high-resolution image of the Balmer line filament in the northwest (NW) quadrant shows that 0.25 < n_0 < le$ 0.4 cm-3 and that the scale along the line of sight is about 2 x 10^{18} cm, while bright features within the filament correspond to ripples with radii of curvature less than 1/10 that size. The derived densities are within the broad range of earlier density estimates, and they agree well with the ionization time scale derived from the Chandra X-ray spectrum of a region just behind the optical filament. This provides a test for widely used models of the X-ray emission from SNR shocks. The scale and amplitude of the ripples are consistent with expectations for a shock propagating though interstellar gas with ~ 20% density fluctuations on parsec scales as expected from studies of interstellar turbulence. One bulge in the filament corresponds to a knot of ejecta overtaking the blast wave, however. The interaction results from the rapid deceleration of the blast wave as it encounters an interstellar cloud.Comment: 16 pages, 6 figures, to appear in Ap

Some constructions of almost para-hyperhermitian structures on manifolds and tangent bundles

In this paper we give some examples of almost para-hyperhermitian structures on the tangent bundle of an almost product manifold, on the product manifold $M\times\mathbb{R}$, where $M$ is a manifold endowed with a mixed 3-structure and on the circle bundle over a manifold with a mixed 3-structure.Comment: 10 pages; This paper has been presented in the "4th German-Romanian Seminar on Geometry" Dortmund, Germany, 15-18 July 200