@inproceedings{3555, abstract = {A sliver is a tetrahedron whose four vertices lie close to a plane and whose perpendicular projection to that plane is a convex quadrilateral with no short edge. Slivers are both undesirable and ubiquitous in 3-dimensional Delaunay triangulations. Even when the point-set is well-spaced, slivers may result. This paper shows that such a point set permits a small perturbation whose Delaunay triangulation contains no slivers. It also gives deterministic algorithms that compute the perturbation of n points in time O(n log n) with one processor and in time O(log n) with O(n) processors.}, author = {Edelsbrunner, Herbert and Li, Xiang and Miller, Gary and Stathopoulos, Andreas and Talmor, Dafna and Teng, Shang and Üngör, Alper and Walkington, Noel}, booktitle = {Proceedings of the 32nd annual ACM symposium on Theory of computing}, isbn = {9781581131840}, location = {Portland, OR, USA}, pages = {273 -- 277}, publisher = {ACM}, title = {{Smoothing and cleaning up slivers}}, doi = {10.1145/335305.335338}, year = {2000}, } @inbook{3572, abstract = {Allzulange wurde die spielhafte Beschäftigung als Gegensatz zu ernsthafter Arbeit gesehen. Dieser Artikel propagiert die spielerische Untersuchung von Kreis- und Kugelmengen. Gleichzeitig belegt er die nutzbare Anwendung von elementaren Einsichten in der Molekularbiologie und allgemeiner in der Beschreibung von Form und Verformung.}, author = {Edelsbrunner, Herbert}, booktitle = {Zur Kunst des formalen Denkens}, isbn = {3851653580}, pages = {153 -- 171}, publisher = {Passagen Verlag}, title = {{Spielereien mit Kreisen und Kugeln. Zum Thema Form und Verformung}}, year = {2000}, } @article{3583, abstract = {The Delaunay triangulation of a finite point set is a central theme in computational geometry. It finds its major application in the generation of meshes used in the simulation of physical processes. This paper connects the predominantly combinatorial work in classical computational geometry with the numerical interest in mesh generation. It focuses on the two- and three-dimensional case and covers results obtained during the twentieth century.}, author = {Edelsbrunner, Herbert}, journal = {Acta Numerica}, pages = {133 -- 213}, publisher = {Cambridge University Press}, title = {{Triangulations and meshes in computational geometry}}, doi = {10.1017/S0962492900001331}, volume = {9}, year = {2000}, } @article{3623, abstract = {We present the theoretical background to a new method for measuring genetic variation for total fitness in Drosophila. The method allows heterozygous effects on total fitness of whole wild-type chromosomes to be measured under normal demography with overlapping generations. The wild-type chromosomes are competed against two balancer chromosomes (B1, B2, say), providing a standard genotype B1/B2 against which variation in the fitness effects of the wild-type chromosomes can be assessed. Fitness can be assessed in two ways: (i) at equilibrium of all three chromosomes under heterozygote advantage, and (ii) during displacement of one balancer by the other. Equilibrium with all three chromosomes present will be achieved only if the wild-type homozygote is not too fit, and if the fitnesses of the three heterozygotes are not too unequal. These conditions were not satisfied for any of a sample of 12 lethal-bearing chromosomes isolated from a random-bred laboratory population of Drosophila. At equilibrium, genotypic frequencies show low sensitivity to changes in genotypic fitness. Furthermore, where all four genotypes are viable and fertile, supplementary information from cages with only two chromosomes present and from direct measurements of pre-adult viability are required to estimate fitnesses from frequencies. The invasion method has the advantages of a greater sensitivity and of not requiring further data to estimate fitnesses if the wild-type homozygote is fertile. However, it requires that multiple samples be taken as the invasion progresses. In a discrete generation model, generation time influences fitness estimates from this method and is difficult to estimate accurately from the data. A full age-structured model can also be applied to the data from both types of experiment. For the invasion method, this gives fitness estimates close to those from the discrete generation model.}, author = {Barton, Nicholas H and Patridge, Linda}, issn = {0016-6723}, journal = {Genetical Research}, number = {3}, pages = {297 -- 314}, publisher = {Cambridge University Press}, title = {{Measuring fitness by means of balancer chromosomes}}, doi = {10.1017/S0016672399004346}, volume = {75}, year = {2000}, } @article{3624, abstract = {The state of a diploid population segregating for two alleles at each of n loci is described by 22(n) genotype frequencies, or equivalently, by allele frequencies and by multilocus moments or cumulants of various orders. These measures of linkage disequilibrium cannot usually be determined, both because one cannot tell whether a gene came from the maternal or paternal gamete, and because such a large number of parameters cannot be estimated even from large samples. Simplifying assumptions must therefore be made. This paper sets out methods for estimating multilocus genotype frequencies which are appropriate for unlinked neutral loci, and for populations that are ultimately derived by mixing of two source populations. In such a hybrid population, all multilocus associations depend primarily on the number of loci involved that derive from the maternal genome, and the number derived from the paternal genome Allele frequencies may differ across loci, and the contribution of each locus to multilocus associations may be scaled by the difference in allele frequency between source populations for that locus (δp ≤ 1). For example, the cumulant describing the association between genes i, j, k from the maternal genome, and genes i, l from the paternal genome is K(tJ,k,iλ*), = δp(i)/2 δp(J) δp(k) δp(l) κ3,2. The state of the population is described by n allele frequencies; n divergences, δp; and by a symmetric matrix of cumulants, κ(J,K) (J = 0 ,..., n, K = 0 ,..., n). Expressions for these cumulants under short- and long-range migration are given. Two methods for estimating the cumulants are described: a simple method based on multivariate moments, and a maximum likelihood procedure, which uses the Metropolis algorithm. Both methods perform well when tested against simulations with two or four loci.}, author = {Barton, Nicholas H}, issn = {0018-067X}, journal = {Heredity}, number = {3}, pages = {373 -- 389}, publisher = {Nature Publishing Group}, title = {{Estimating multilocus linkage disequilibria}}, doi = {10.1046/j.1365-2540.2000.00683.x}, volume = {84}, year = {2000}, } @article{3798, abstract = {Glutamate is the main excitatory transmitter in the mammalian CNS, mediating fast synaptic transmission primarily by activation of AMPA-type glutamate receptor channels. Both synaptic structure and a cell-specific molecular switch in the AMPA receptor subunit expression are involved in the regulation of the synaptic signaling time course.}, author = {Jonas, Peter M}, issn = {1548-9213}, journal = {Physiology}, number = {2}, pages = {83 -- 89}, publisher = {American Physiological Society}, title = {{The time course of signaling at central glutamatergic synapses}}, doi = {10.1152/physiologyonline.2000.15.2.83}, volume = {15}, year = {2000}, } @article{3923, author = {Cremer, Sylvia}, issn = {0179-6372}, journal = {Futura: the Journal of the Boehringer Ingelheim Fonds}, number = {1}, pages = {68 -- 71}, publisher = {Hippokrates}, title = {{Paternity analysis with AFLPs in Cardiocondyla ants}}, volume = {15}, year = {2000}, } @article{4004, abstract = {In this paper we introduce the abacus model of a simplex and use it to subdivide a d-simplex into k(d) d-simplices all of the same volume and shape characteristics. The construction is an extension of the subdivision method of Freudenthal [3] and has been used by Goodman and Peters [4] to design smooth manifolds.}, author = {Edelsbrunner, Herbert and Grayson, Daniel}, issn = {0179-5376}, journal = {Discrete & Computational Geometry}, number = {4}, pages = {707 -- 719}, publisher = {Springer}, title = {{Edgewise subdivision of a simplex}}, doi = {10.1007/s004540010063}, volume = {24}, year = {2000}, } @inproceedings{4008, abstract = {We formalize a notion of topological simplification within the framework of a filtration, which is the history of a growing complex. We classify a topological change that happens during growth as either a feature or noise depending on its life-time or persistence within the filtration. We give fast algorithms for computing persistence and experimental evidence for their speed and utility.}, author = {Edelsbrunner, Herbert and Letscher, David and Zomorodian, Afra}, booktitle = {Proceedings 41st Annual Symposium on Foundations of Computer Science}, isbn = {0769508502}, location = {Washington, DC, United States}, pages = {454 -- 463}, publisher = {IEEE}, title = {{Topological persistance and simplification}}, doi = {10.1109/SFCS.2000.892133}, year = {2000}, } @article{4009, abstract = {We study the maintenance of a simplicial grid or complex under changing density requirements. The proposed method works in any fixed dimension and generates grids by projecting cross-sections of a monotone simplicial complex that lives in one dimension higher than the grid. The density of the grid is adapted by locally moving the cross-section up or down along the extra dimension.}, author = {Edelsbrunner, Herbert and Waupotitsch, Roman}, issn = {0218-1959}, journal = {International Journal of Computational Geometry and Applications}, number = {3}, pages = {267 -- 284}, publisher = {World Scientific Publishing}, title = {{Adaptive simplicial grids from cross-sections of monotone complexes}}, doi = {10.1142/S0218195900000164}, volume = {10}, year = {2000}, } @article{4010, abstract = {A sliver is a tetrahedron whose four vertices lie close to a plane and whose orthogonal projection to that plane is a convex quadrilateral with no short edge. Slivers are notoriously common in 3-dimensional Delaunay triangulations even for well-spaced point sets. We show that, if the Delaunay triangulation has the ratio property introduced in Miller et al. [1995], then there is an assignment of weights so the weighted Delaunay triangulation contains no slivers. We also give an algorithm to compute such a weight assignment.}, author = {Cheng, Siu and Dey, Tamal and Edelsbrunner, Herbert and Facello, Michael and Teng, Shang}, issn = {0004-5411}, journal = {Journal of the ACM}, number = {5}, pages = {883 -- 904}, publisher = {ACM}, title = {{Sliver exudation}}, doi = {10.1145/355483.355487}, volume = {47}, year = {2000}, } @article{4147, abstract = {We have developed a protocol to perform a genetic screen for zygotic mutations affecting embryogenesis on the protochordate Ciona intestinalis. The choice of this taxon, whose phylogenetic position places it at the basis of the chordates as one the most primitive vertebrate relatives, could allow to address several evolutionary questions. The protochordates share many morphological features with the vertebrates, in primis the presence of a notochord. Ciona intestinalis shows several ideal features for a mutational analysis, such as external development and larvae made of a limited number of cells and cell types. Detailed cell lineage studies are available. The haploid genome size is comparable to the size of the Drosophila haploid genome. We have optimised conditions for chemical mutagenesis studying the efficiency at which different concentration of N-ethyl-N-nitrosourea (ENU) can induce mutations. Because the adult Ciona are hermaphrodites, we are performing a one-generation screen. The induced mutations are identified by visual inspection of developmental stages. We report the preliminary results from our screen including examples of the different classes of mutant phenotypes found so far.}, author = {Sordino, Paolo and Heisenberg, Carl-Philipp J and Cirino, Paola and Toscano, Alfonso and Giuliano, Paola and Marino, Rita and Pinto, Maria and De Santis, Rosaria}, issn = {0036-4827}, journal = {Sarsia}, number = {2}, pages = {173 -- 176}, publisher = {Taylor & Francis}, title = {{A mutational approach to the study of development of the protochordate Ciona intestinalis (Tunicata, Chordata)}}, doi = {10.1080/00364827.2000.10414567}, volume = {85}, year = {2000}, } @article{4197, abstract = {Vertebrate gastrulation involves the specification and coordinated movement of large populations of cells that give rise to the ectodermal, mesodermal and endodermal germ layers. Although many of the genes involved in the specification of cell identity during this process have been identified, little is known of the genes that coordinate cell movement. Here we show that the zebrafish silberblick (slb) locus(1) encodes Wnt11 and that Slb/Wnt11 activity is required for cells to undergo correct convergent extension movements during gastrulation. In the absence of Slb/Wnt11 function, abnormal extension of axial tissue results in cyclopia and other midline defects in the head(2). The requirement for Slb/Wnt11 is cell non-autonomous, and our results indicate that the correct extension of axial tissue is at least partly dependent on medio-lateral cell intercalation in paraxial tissue. We also show that the slb phenotype is rescued by a truncated form of Dishevelled that does not signal through the canonical Wnt pathway(3), suggesting that, as in flies(4), Wnt signalling might mediate morphogenetic events through a divergent signal transduction cascade. Our results provide genetic and experimental evidence that Wnt activity in lateral tissues has a crucial role in driving the convergent extension movements underlying vertebrate gastrulation.}, author = {Heisenberg, Carl-Philipp J and Tada, Masazumi and Rauch, Gerd and Saúde, Leonor and Concha, Miguel and Geisler, Robert and Stemple, Derek and Smith, James and Wilson, Stephen}, issn = {0028-0836}, journal = {Nature}, number = {6782}, pages = {76 -- 81}, publisher = {Nature Publishing Group}, title = {{Silberblick/Wnt11 mediates convergent extension movements during zebrafish gastrulation}}, doi = {10.1038/35011068}, volume = {405}, year = {2000}, } @misc{4268, author = {Partridge, Linda and Barton, Nicholas H}, booktitle = {Nature}, issn = {0028-0836}, number = {6803}, pages = {457 -- 458}, publisher = {Nature Publishing Group}, title = {{Evolving evolvability}}, doi = {10.1038/35035173}, volume = {407}, year = {2000}, } @article{4269, author = {Coyne, Jerry and Barton, Nicholas H and Turelli, Michael}, issn = {0014-3820}, journal = {Evolution; International Journal of Organic Evolution}, number = {1}, pages = {306 -- 317}, publisher = {Wiley-Blackwell}, title = {{Is Wright’s shifting balance process important in evolution?}}, doi = {10.1554/0014-3820(2000)054[0306:IWSSBP]2.0.CO;2}, volume = {54}, year = {2000}, } @article{4270, abstract = {A coalescence-based maximum-likelihood method is presented that aims to (i) detect diversity-reducing events in the recent history of a population and (ii) distinguish between demographic (e.g., bottlenecks) and selective causes (selective sweep) of a recent reduction of genetic variability. The former goal is achieved by taking account of the distortion in the shape of gene genealogies generated by diversity-reducing events: gene trees tend to be more star-like than under the standard coalescent. The latter issue is addressed by comparing patterns between loci: demographic events apply to the whole genome whereas selective events affect distinct regions of the genome to a varying extent. The maximum-likelihood approach allows one to estimate the time and strength of diversity-reducing events and to choose among competing hypotheses. An application to sequence data from an African population of Drosophila melanogaster shows that the bottleneck hypothesis is unlikely and that one or several selective sweeps probably occurred in the recent history of this population.}, author = {Galtier, Nicolas and Depaulis, Frantz and Barton, Nicholas H}, issn = {0016-6731}, journal = {Genetics}, number = {2}, pages = {981 -- 987}, publisher = {Genetics Society of America}, title = {{Detecting bottlenecks and selective sweeps from DNA sequence polymorphism}}, doi = {10.1093/genetics/155.2.981}, volume = {155}, year = {2000}, } @article{4271, abstract = {Within hybrid zones that are maintained by a balance between selection and dispersal, linkage disequilibrium is generated by the mixing of divergent populations. This linkage disequilibrium causes selection on each locus to act on all other loci, thereby steepening dines, and generating a barrier to gene flow. Diffusion models predict simple relations between the strength of linkage disequilibrium and the dispersal rate, σ, and between the barrier to gene flow, B, and the reduction in mean fitness, W̄. The aim of this paper is to test the accuracy of these predictions by comparison with an exact deterministic model of unlinked loci (r = 0.5). Disruptive selection acts on the proportion of alleles from the parental populations (p, q): W = exp[-S(4pq)(β)], such that the least fit genotype has fitness e(-S). Where β << 1, fitness is reduced for a wide range of intermediate genotypes; where β >> 1, fitness is only reduced for those genotypes close to p = 0.5. Even with strong epistasis, linkage disequilibria are close to σ2p'(i)p'(j)/r(ij), where p'(i), p'(j) are the gradients in allele frequency at loci i, j. The barrier to gene flow, which is reflected in the steepening of neutral dines, is given by B = ∫(-∞)(∞) (W̄(1/r̄)-1) dx, where r̄, the harmonic mean recombination rate between the neural and selected loci, is here 0.5. This is a close approximation for weak selection, but underestimates B for strong selection. The barrier is stronger for small β, because hybrid fitness is then reduced over a wider range of p. The widths of the selected dines are harder to predict: though simple approximations are accurate for β = 1, they become inaccurate for extreme β because, then, fitness changes sharply with p. Estimates of gene number, made from neutral dines on the assumption that selection acts against heterozygotes, are accurate for weak selection when β = 1; however, for strong selection, gene number is overestimated. For β > 1, gene number is systematically overestimated and, conversely, when β < 1, it is underestimated. }, author = {Barton, Nicholas H and Shpak, Max}, issn = {0016-6723}, journal = {Genetical Research}, number = {2}, pages = {179 -- 198}, publisher = {Cambridge University Press}, title = {{The effects of epistasis on the structure of hybrid zones}}, doi = {10.1017/S0016672399004334}, volume = {75}, year = {2000}, } @article{4272, abstract = {Analysis of multilocus evolution is usually intractable for more than n ~ 10 genes, because the frequencies of very large numbers of genotypes must be followed. An exact analysis of up to n ~ 100 loci is feasible for a symmetrical model, in which a set of unlinked loci segregate for two alleles (labeled '0' and '1') with interchangeable effects on fitness. All haploid genotypes with the same number of 1 alleles can then remain equally frequent. However, such a symmetrical solution may be unstable: for example, under stabilizing selection, populations tend to fix any one genotype which approaches the optimum. Here, we show how the 2' x 2' stability matrix can be decomposed into a set of matrices, each no larger than n x n. This allows the stability of symmetrical solutions to be determined. We apply the method to stabilizing and disruptive selection in a single deme and to selection against heterozygotes in a linear cline. (C) 2000 Academic Press.}, author = {Barton, Nicholas H and Shpak, Max}, issn = {0040-5809}, journal = {Theoretical Population Biology}, number = {3}, pages = {249 -- 263}, publisher = {Academic Press}, title = {{The stability of symmetrical solutions to polygenic models}}, doi = {10.1006/tpbi.2000.1455}, volume = {57}, year = {2000}, } @article{4273, abstract = {We review the various factors that limit adaptation by natural selection. Recent discussion of constraints on selection and, conversely, of the factors that enhance 'evolvability', have concentrated on the kinds of variation that can be produced. Here, we emphasise that adaptation depends on how the various evolutionary processes shape variation in populations. We survey the limits that population genetics places on adaptive evolution, and discuss the relationship between disparate literatures. BioEssays 22:1075-1084, 2000. (C) 2000 John Wiley and Sons, Inc.}, author = {Barton, Nicholas H and Partridge, Linda}, issn = {0265-9247}, journal = {BioEssays}, number = {12}, pages = {1075 -- 1084}, publisher = {Wiley-Blackwell}, title = {{Limits to natural selection}}, doi = {10.1002/1521-1878(200012)22:12<1075::AID-BIES5>3.0.CO;2-M}, volume = {22}, year = {2000}, } @article{4274, abstract = {Selection on one or more genes inevitably perturbs other genes, even when those genes have no direct effect on fitness. This article reviews the theory of such genetic hitchhiking, concentrating on effects on neutral loci. Maynard Smith and Haigh introduced the classical case where the perturbation is due to a single favourable mutation. This is contrasted with the apparently distinct effects of inherited variation in fitness due to loosely linked loci. A model of fluctuating selection is analysed which bridges these alternative treatments. When alleles sweep between extreme frequencies at a rate λ, the rate of drift is increased by a factor (1 + E[1/pq]λ/(2(2λ + r))), where the recombination rate r is much smaller than the strength of selection. In spatially structured populations, the effects of any one substitution are weaker, and only cause a local increase in the frequency of a neutral allele. This increase depends primarily on the rate of recombination relative to selection (r/s), and more weakly, on the neighbourhood size, Nb = 4πρσ2. Spatial subdivision may allow local selective sweeps to occur more frequently than is indicated by the overall rate of molecular evolution. However, it seems unlikely that such sweeps can be sufficiently frequent to increase significantly the drift of neutral alleles.}, author = {Barton, Nicholas H}, issn = {0962-8436}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1403}, pages = {1553 -- 1562}, publisher = {Royal Society of London}, title = {{Genetic hitchhiking}}, doi = {10.1098/rstb.2000.0716}, volume = {355}, year = {2000}, }