The Phenotype-Fitness Map in Experimental Evolution of Phages

Evolutionary biologists commonly interpret adaptations of organisms by reference to a phenotype-fitness map, a model of how different states of a phenotype affect fitness. Notwithstanding the popularity of this approach, it remains difficult to directly test these mappings, both because the map often describes only a small subset of phenotypes contributing to total fitness and because direct measures of fitness are difficult to obtain and compare to the map. Both limitations can be overcome for bacterial viruses (phages) grown in the experimental condition of unlimited hosts. A complete accounting of fitness requires 3 easily measured phenotypes, and total fitness is also directly measurable for arbitrary genotypes. Yet despite the presumed transparency of this system, directly estimated fitnesses often differ from fitnesses calculated from the phenotype-fitness map. This study attempts to resolve these discrepancies, both by developing a more exact analytical phenotype-fitness map and by exploring the empirical foundations of direct fitness estimates. We derive an equation (the phenotype-fitness map) for exponential phage growth that allows an arbitrary distribution of lysis times and burst sizes. We also show that direct estimates of fitness are, in many cases, plausibly in error because the population has not attained stable age distribution and thus violates the model underlying the phenotype-fitness map. In conjunction with data provided here, the new understanding appears to resolve a discrepancy between the reported fitness of phage T7 and the substantially lower value calculated from its phenotype-fitness map

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

The relative contributions of neutral and adaptive substitutions to molecular evolution has been one of the most controversial issues in evolutionary biology for more than 40 years. The analysis of within-species nucleotide polymorphism and between-species divergence data supports a widespread role for adaptive protein evolution in certain taxa. For example, estimates of the proportion of adaptive amino acid substitutions (alpha) are 50% or more in enteric bacteria and Drosophila. In contrast, recent estimates of alpha for hominids have been at most 13%. Here, we estimate alpha for protein sequences of murid rodents based on nucleotide polymorphism data from multiple genes in a population of the house mouse subspecies Mus musculus castaneus, which inhabits the ancestral range of the Mus species complex and nucleotide divergence between M. m. castaneus and M. famulus or the rat. We estimate that 57% of amino acid substitutions in murids have been driven by positive selection. Hominids, therefore, are exceptional in having low apparent levels of adaptive protein evolution. The high frequency of adaptive amino acid substitutions in wild mice is consistent with their large effective population size, leading to effective natural selection at the molecular level. Effective natural selection also manifests itself as a paucity of effectively neutral nonsynonymous mutations in M. m. castaneus compared to humans

Search for Electroweak Production of Single Top Quarks in ppbar Collisions

We present a search for electroweak production of single top quarks in the electron+jets and muon+jets decay channels. The measurements use ~90 pb^-1 of data from Run 1 of the Fermilab Tevatron collider, collected at 1.8 TeV with the DZero detector between 1992 and 1995. We use events that include a tagging muon, implying the presence of a b jet, to set an upper limit at the 95% confidence level on the cross section for the s-channel process ppbar->tb+X of 39 pb. The upper limit for the t-channel process ppbar->tqb+X is 58 pb.Comment: 11 pages, 2 figures. This is the published versio

Probing BFKL Dynamics in the Dijet Cross Section at Large Rapidity Intervals in ppbar Collisions at sqrt{s}=1800 and 630 GeV

Inclusive dijet production at large pseudorapidity intervals (delta_eta) between the two jets has been suggested as a regime for observing BFKL dynamics. We have measured the dijet cross section for large delta_eta in ppbar collisions at sqrt{s}=1800 and 630 GeV using the DO detector. The partonic cross section increases strongly with the size of delta_eta. The observed growth is even stronger than expected on the basis of BFKL resummation in the leading logarithmic approximation. The growth of the partonic cross section can be accommodated with an effective BFKL intercept of a_{BFKL}(20GeV)=1.65+/-0.07.Comment: Published in Physical Review Letter

Search for Large Extra Dimensions in Dielectron and Diphoton Production

We report a search for effects of large extra spatial dimensions in ppbar collisions at a center-of-mass energy of 1.8 TeV with the DZero detector, using events containing a pair of electrons or photons. The data are in good agreement with the expected background and do not exhibit evidence for large extra dimensions. We set the most restrictive lower limits to date, at the 95% confidence level, on the effective Planck scale between 1.0 TeV and 1.4 TeV for several formalisms and numbers of extra dimensions.Comment: 6 pages, 2 figures, submitted to Phys. Rev. Let

Search for R-parity Violating Supersymmetry in Dimuon and Four-Jets Channel

We present results of a search for R-parity-violating decay of the neutralino chi_1^0, taken to be the Lightest Supersymmetric Particle. It is assumed that this decay proceeds through one of the lepton-number violating couplings lambda-prime_2jk (j=1,2; k=1,2,3). This search is based on 77.5 pb-1 of data, collected by the D0 experiment at the Fermilab Tevatron in ppbar collisions at a center of mass energy of 1.8 TeV in 1992-1995.Comment: 10 pages, 3 figure

Spin Correlation in tt-bar Production from pp-bar Collisions at sqrt(s)=1.8 TeV

The D0 collaboration has performed a study of spin correlation in tt-bar production for the process tt-bar to bb-bar W^+W^-, where the W bosons decay to e-nu or mu-nu. A sample of six events was collected during an exposure of the D0 detector to an integrated luminosity of approximately 125 pb^-1 of sqrt{s}=1.8 TeV pp-bar collisions. The standard model (SM) predicts that the short lifetime of the top quark ensures the transmission of any spin information at production to the tt-bar decay products. The degree of spin correlation is characterized by a correlation coefficient k. We find that k>-0.25 at the 68% confidence level, in agreement with the SM prediction of k=0.88.Comment: Submitted to PRL, Added references, minor changes to tex

A Quasi-Model-Independent Search for New Physics at Large Transverse Momentum

We apply a quasi-model-independent strategy ("Sleuth") to search for new high p_T physics in approximately 100 pb^-1 of ppbar collisions at sqrt(s) = 1.8 TeV collected by the DZero experiment during 1992-1996 at the Fermilab Tevatron. Over thirty-two e mu X, W+jets-like, Z+jets-like, and 3(lepton/photon)X exclusive final states are systematically analyzed for hints of physics beyond the standard model. Simultaneous sensitivity to a variety of models predicting new phenomena at the electroweak scale is demonstrated by testing the method on a particular signature in each set of final states. No evidence of new high p_T physics is observed in the course of this search, and we find that 89% of an ensemble of hypothetical similar experimental runs would have produced a final state with a candidate signal more interesting than the most interesting observed in these data.Comment: 28 pages, 17 figures. Submitted to Physical Review

Search for Second Generation Leptoquark Pairs in pbar-p Collisions at sqrt(s) = 1.8 TeV

We have searched for second generation leptoquark (LQ) pairs in the \mu\mu+jets channel using 94+-5 pb^{-1} of pbar-p collider data collected by the D0 experiment at the Fermilab Tevatron during 1993-1996. No evidence for a signal is observed. These results are combined with those from the \mu\nu+jets and \nu\nu+jets channels to obtain 95% confidence level (C.L.) upper limits on the LQ pair production cross section as a function of mass and $beta, the branching fraction of a LQ decay into a charged lepton and a quark. Lower limits of 200(180) GeV/c^2 for \beta=1(1/2) are set at the 95% C.L. on the mass of scalar LQ. Mass limits are also set on vector leptoquarks as a function of \beta.Comment: 6 pages, 4 figures. Submitted to Phys. Rev. Let

Precise measurement of the top quark mass in the dilepton channel at D0

We measure the top quark mass (mt) in ppbar collisions at a center of mass energy of 1.96 TeV using dilepton ttbar->W+bW-bbar->l+nubl-nubarbbar events, where l denotes an electron, a muon, or a tau that decays leptonically. The data correspond to an integrated luminosity of 5.4 fb-1 collected with the D0 detector at the Fermilab Tevatron Collider. We obtain mt = 174.0 +- 1.8(stat) +- 2.4(syst) GeV, which is in agreement with the current world average mt = 173.3 +- 1.1 GeV. This is currently the most precise measurement of mt in the dilepton channel.Comment: 7 pages, 4 figure