@inproceedings{3551, abstract = {Common geometric models for proteins and other molecules are the space filling diagram, the solvent accessible surface, and the molecular surface. We describe software that computes metric properties of these models, including volume and surface area. It also measures voids or empty space enclosed by the protein, and it keeps track of surface area contributions of individual atoms. The software is based on 3-dimensional alpha complexes and on inclusion-exclusion formulas with terms derived from the simplices in this complex.}, author = {Edelsbrunner, Herbert and Facello, Michael and Fu, Ping and Liang, Jie}, booktitle = {Proceedings of the 28th Annual Hawaii International Conference on System Sciences}, isbn = {0-8186-6930-6}, location = {Wailea, HI, United States of America}, pages = {256 -- 264}, publisher = {IEEE}, title = {{Measuring proteins and voids in proteins}}, doi = {10.1109/HICSS.1995.375331}, year = {1995}, } @inproceedings{3552, abstract = {The concept of an α-shape of a finite set of points in R^d, with weights, is defined and illustrated. An α-shape is a polytope which is not necessarily convex nor connected and can be derived from the (weighted) Delaunay triangulation of the point set, with a parameter controlling the desired level of detail. The set of all α values leads to a descrete family of shapes capturing the intuitive notion of ``crude'' versus ``fine'' shapes of a point set. Software that computes such shapes in R^2 and R^3 is available via anonymous ftp from: ftp://ftp.ncsa.uiuc.edu/Visualization/Alpha-shape/ }, author = {Akkiraju, Nataraj and Edelsbrunner, Herbert and Facello, Michael and Fu, Ping and Mücke, Ernst and Varela, Carlos}, pages = {63 -- 66}, publisher = {Elsevier}, title = {{Alpha shapes: definition and software}}, year = {1995}, } @article{3636, abstract = {Observations on the means, variances, and covariances of quantitative traits across hybrid zones can give information similar to that from Mendelian markers. In addition, they can identify particular traits through which the cline is maintained. We describe a survey of six traits across the hybrid zone between Bombina bombina and Bombina variegata (Amphibia: Discoglossidae) near Pescenica in Croatia. We obtained laboratory measuments of the belly pattern, skin thickness, mating call, skeletal form, egg size, and the developmental time of tadpoles. Although offspring from hybrid populations showed no evidence of reduced viability, a third of the F1 families failed completely, irrespective of the direction of the cross. All traits differed significantly between the taxa. Clines in belly pattern, skin thickness, mating call, and skeletal form were closely concordant with clines in four diagnostic enzyme loci. However, the cline in developmental time was displaced towards bombina, and the cline in egg size was displaced towards variegata. This discordance could be because the traits are not inherited additively or because they are subject to different selection pressures. We favor the latter explanation in the case of developmental time. We show that moderate selection acting directly on a trait suffices to shift its position; rather stronger selection is needed to change its width appreciably. Within hybrid populations, there are significant associations among quantitative traits, and between traits and enzymes. Phenotypic variances also increase in hybrid populations. These observations can be explained by linkage disequilibria among the underlying loci. However, the average magnitude of the covariance between traits is about half that expected from the linkage disequilibria between enzyme loci. The discrepancy is not readily explained by nonadditive gene action. This puzzle is now unresolved and calls for further investigation.}, author = {Nürnberger, Beate and Barton, Nicholas H and Maccallum, Catriona and Gilchrist, Jason and Appleby, Michael}, issn = {0014-3820}, journal = {Evolution}, number = {6}, pages = {1224 -- 1238}, publisher = {Wiley-Blackwell}, title = {{Natural selection on quantitative traits in the Bombina hybrid zone}}, doi = {10.1111/j.1558-5646.1995.tb04449.x}, volume = {49}, year = {1995}, } @article{3637, abstract = {Hybridizing taxa remain distinct for two main reasons. Natural selection acts against hybrids either because of their incompatible genome, or because of differential adaptation of the pure types across an environmental gradient. Here, we provide experimental evidence that the location of the Bombina (Anura: Discoglossidae) hybrid zone in Croatia is, at least in part, determined by differential adaptation. B. bombina typically breeds in permanent water in the lowland, whereas B. variegata reproduces in puddles at higher elevations. In a reciprocal translocation, pure bombina and variegata tadpoles were introduced in equal proportions into lowland pond enclosures and upland puddles. After three weeks, variegata exceeded bombina in survival and growth in both habitats. The effect was most pronounced in puddles, where the few surviving bombina tadpoles had hardly grown at all. In comparison to variegata, the smaller hatchlings of bombina grew relatively faster in ponds, but remained smaller in absolute terms. Nevertheless, B. bombina appears better adapted to ponds than to puddles. The mechanisms by which variegata is excluded from ponds remain to be demonstrated. These data show that habitat dependent selection prevents the invasion of bombina tadpole traits into the variegata gene pool. Given the strong linkage disequilibria in hybrid populations, differential selection on tadpoles may be sufficient to maintain the integrity of the two gene pools.}, author = {Maccallum, Catriona and Nürnberger, Beate and Barton, Nicholas H}, issn = {0962-8452}, journal = {Proceedings of the Royal Society of London Series B Biological Sciences}, number = {1359}, pages = {257 -- 264}, publisher = {Royal Society of London}, title = {{Experimental evidence for habitat dependent selection in a Bombina hybrid zone}}, doi = {10.1098/rspb.1995.0089}, volume = {260}, year = {1995}, } @article{3639, abstract = {A general representation of multilocus selection is extended to allow recombination to depend on genotype. The equations simplify if modifier alleles have small effects on recombination. The evolution of such modifiers only depends on how they alter recombination between the selected loci, and does not involve dominance in modifier effects. The net selection on modifiers can be found explicitly if epistasis is weak relative to recombination. This analysis shows that recombination can be favoured in two ways: because it impedes the response to epistasis which fluctuates in sign, or because it facilitates the response to directional selection. The first mechanism is implausible, because epistasis must change sign over periods of a few generations: faster or slower fluctuations favour reduced recombination. The second mechanism requires weak negative epistasis between favourable alleles, which may either be increasing, or held in check by mutation. The selection (si) on recombination modifiers depends on the reduction in additive variance of log (fitness) due to linkage disequilibria (υ1 < 0), and on non-additive variance in log (fitness) (V′2, V′3,.. epistasis between 2, 3.. loci). For unlinked loci and pairwise epistasis, si = − (υ1 + 4V2/3)δr, where δr is the average increase in recombination caused by the modifier. The approximations are checked against exact calculations for three loci, and against Charlesworth's analyses of mutation/selection balance (1990), and directional selection (1993). The analysis demonstrates a general relation between selection on recombination and observable components of fitness variation, which is open to experimental test.}, author = {Barton, Nicholas H}, issn = {0016-6723}, journal = {Genetical Research}, number = {2}, pages = {123 -- 144}, publisher = {Cambridge University Press}, title = {{A general model for the evolution of recombination}}, doi = {10.1017/S0016672300033140}, volume = {65}, year = {1995}, }