YIBS Five Year Report

Publications Resulting from YIBS Center Research: 1991-1995

Books

Center for Global Change
CGC 8: Turekian, K.K. (1995). Global Environmental Change: Past Present and Future. Prentice Hall, Upper Saddle River, NJ.

Center for ECOSAVE
CE 5: Vrba, E. S., Denton, G. H., Partridge, T. C. & L. H. Burckle (1994). Paleoclimate and evolution with emphasis on human origins. Yale University Press, New Haven, CT. in press.

Articles

Center For Biological Transformation
CBT a: DiMarco, A. A., Averhoff, B., & L. N. Ornston (1993). Identification of the transcriptional activator pobR, and characterization of its role in the expression of pobA, the structural gene for p-hydroxybenzoate hydroxylase in Acinetobacter calcoaceticus. J. Bacteriol. 175: 4499-4506.

CBT 1: Shanley, M. S., Harrison, A., Parales, R. E., Kowalchuk, G., Mitchell, D. J., & L. N. Ornston (1994). Unusual G+C content and codon usage in catIJF, a segment of the ben-cat supra-operonic cluster in the Acinetobacter calcoaceticus chromosome. Gene 138: 59-65.

CBT 2: Hartnett, G. B. & L. N. Ornston (1994). Acquisition of apparent DNA slippage structures during extensive evolutionary divergence of pcaD and catD, genes for enzymes with identical catalytic activities in Acinetobacter calcoaceticus. Gene 142: 23-29.

CBT 3: Gregg-Jolly, L. A. & L. N. Ornston (1994). Properties of Acinetobacter calcoaceticus recA and its contribution to intracellular gene conversion. Mol. Microbiol. 12: 985-982.

CBT 4: DiMarco, A. A. & L. N. Ornston (1994). Regulation of p-hydroxybenzoate hydroxylase synthesis by pobR bound to an operator in Acinetobacter calcoaceticus. J. Bacteriol. 176: 4277-4284.

CBT 5: Kowalchuk, G. A., Hartnett, G. B., Benson, A., Houghton, J. E., Ngai, K. L. & L. N. Ornston (1994). Contrasting patterns of evolutionary divergence within the Acinetobacter calcoaceticus pca operon. Gene 146: 23-30.

CBT 6: Elsemore, D. & L. N. Ornston (1994). The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for Quinate/Shikimate Dehydrogenase. J. Bacteriol. 176 (24): 7659-7666.

CBT 7: Gerischer, U. & L. N. Ornston (1994). Spontaneous mutations in pcaH,G, structural genes for protocatechuate 3,4-dioxygenase in Acinetobacter calcoaceticus. J. Bacteriol. 177 (5): 1336-1347.

CBT 8: Kolwalchuk, G. A., Gregg-Jolly, L. A. & L. N. Ornston (1994). Nucleotide sequences transferred by gene conversion in the bacterium Acinetobacter calcoaceticus. Gene (Amsterdam) 153 (1): 11-115.

CBT 9: Houghton, J. E., Brown,T. M., Appel, A. J., Hughes, E. J. & L. N. Ornston (1994). Discontinuities in the evolution of Pseudomonas putida cat genes. J. Bacteriol. 177: 401-412.

CBT 10: Fernandez, J., DiMarco, A. A., Ornston, L. N. & S. Harayama (1995). Purification and characterization of Acinetobacter calcoaceticus 4-hydroxybenzoate 3-hydroxylase after its overexpression in Eschereichia coli. J. Bacteriol. 117: 1261-1266.

CBT 11: Elsemore, D. A. & L. N. Ornston (1995). Unusual ancestry of dehydratases associated with quinate catabolism in Acinetobacter calocaceticus. J. Bacteriol. 177 (20): 5971-5978.

CBT 12: Kloos, D.-U., DiMarco, A. A., Elsemore, D. A., Timmis, K. N. & L. N.Ornston (1995). Distance between alleles as a determinant of linkage in natural transformation of Acinetobacter calcoaceticus. J. Bacteriol. 177 (20): 6015-6017.

CBT 13: Gerischer, U., D'Argenio, D. A. & L. N. Ornston (1995). IS1236, a newly discovered member of the IS3 family, exhibits varied patterns of insertion into the Acinetobacter calcoaceticus chromosome. J. Bacteriol. submitted.

CBT 14: Sun, L., Jiang, R-Z., Steinbach, S., Holmes, A., Campanelli, C., Forstner, J., Sajjan, U., Tan, Y., Riley, M. A. & R. Goldstein(1995). The emergence of a highly transmissible lineage of cbl+ Pseudoomonas (Burkholderia) cepacia causing CF centre epidemics in North America and Britain. Nature Medicine v. 1 (7): 661-666.

CBT 15: Wagner, R. R. & M. A. Riley (1995). Low synonymous site variation at the lacY locus in Escherichia coli suggests the action of positive selection. J. Molec. Evol. in press.

CBT 16: Feldgarden, M., Golden, S., Wilson, H. & M. A. Riley (1995). Can phage defense maintain colicin plasmids in Escherichis coli? Journal of Microbiology (Reading) 141 (11): 2977-2984.

Center For Computational Ecology
CCE 1: Reinitz, J., Mjolsness, E. & D. H. Sharp (1992). Model for cooperative control of positional information in Drosophilia by bcd and maternal hb. Research Report YALEU/DCS/RR-922: 1-20.

CCE 2: Mjolsness, E., Garrett, C. D., Reinitz, J. & D. H. Sharp (1993). Modeling the connection between development and evolution: Preliminary report. Research Report YALEU/DCS/TS 979: 1-19.

CCE 3: Fontana, W. & L. W. Buss (1993). "The arrival of the fittest: Toward a theory of biological organization." Bull. of Math. Biol. 56 (1): 1-64.

CCE 4: Buss, L. W. & J. R. Vaisnys (1993). Temperature stress induces dynamical chaos in a cnidarian gastrovascular system. Proc. R. Soc. Lond. B. 252: 39-41.

CCE 5: Fontana, W. & L. W. Buss (1993). What would be conserved if the "tape were run twice?" PNAS, USA, 91: 757-761.

CCE 6: Wagner, G. P. & P. Krall (1993). What is the difference between models of error thresholds and Muller's ratchet? J. Math. Biol. 32: 33-44.

CCE 7: Wagner, A., Wagner, G. P. & P. Similion (1993). Epistasis facilitates the evolution of reproductive isolation by peak shifts: A two locus two-allele model. Genetics 138: 533-545.

CCE 8: Wagner, A. & N. Blackstone (1994). Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. System Biol. 43: 250-261.

CCE 9: Wagner, A. (1994). Evolution of gene networks by gene duplications: A mathematical model and its implications on genome organization. PNAS, USA, 91: 4387-4391.

CCE 10: Fontana, W., Wagner, G. P. & L. W. Buss (1994). Beyond digital naturalism. Artificial Life 1: 211-227.

CCE 11: Fontana, W. & L. W. Buss (1994). Toward a theory of biological organization. Bull. Math. Biol. 56: 1-64.

CCE 12: Dudgeon, S. R. & L. W. Buss (1994). Growing with the flow: On the maintenance and malleability of colony form in the hydroid hydractinia. Amer. Naturalist submitted.

CCE 13: Schmitz, O. J. (1994). Resource edibility and trophic exploitation in an old-field web. PNAS, USA, 91: 5364-6367.

CCE 14: Schmitz, O. J. (1994). Optimal foraging and consumer-resource dynamics. Proceedings of the 6th International Theriological Congress. Sydney, Australia, in press.

CCE 15: Belovsky, G. E. & O. J. Schmitz (1994). Herbivore optimal foraging and plant defenses. Proceedings of the 6th International Theriological Congress, Sydney, Australia, in press.

CCE 16: Wagner, A. (1995). Does evolutionary plasticity evolve? Evolution in press.

CCE 17: Wagner, A. (1995). Can nonlinear epigenetic interactions obscure relations between genotype and phenotype? Nonlinearity submitted.

CCE 18: Schmitz, O. J., Cohon, J. L., Rothley, K. D. & A. P. Berckerman (1995). Adaptive behavior in complex environments: A multiobjective programming approach. Am. Naturalist submitted.

CCE 22: Wagner, G. P. (1994). Evolution of canalization by stabilizing selection: Why genetic and environmental canalization tend to be correlated. CCE-Tech report.

CCE 23: Wagner, G. P. (1995). Homologues, Natural Kinds and the Evolution of modularity. American Zoologist in press.

CCE 24: Schmitz, O. J. & G. Booth (1995). Modeling food web complexity: the consequence of individual-based spatially explicit behavioral ecology on trophic interactions. Evolutionary Ecology submitted.

CCE 25: Wagner, G. P. (1995). Adaptation and the modular design of organisms.8 In F. Morán, A. Morán, J. J. Merelo and P. Chacón (ed.). Advances in Artificial Life. Berlin, Springer pp. 317-32.

CCE 27: Wagner, G. P. & L. Altenberg (1995). Complex Adaptations and the Evolution of Evolvability. Evolution in press.

CCE 30: Wagner, G. P. (1995). Apparent stabilizing selection and the maintenance of neutral genetic variation. Genetics submitted.

CCE 31: Laubichler, M. D. (1995). The semiotics of biological functions. I. Rauch (ed.) Proceedings of the Fifth Congress of the International Association for Semiotic Studies, Berkeley, Mouton de Gryter, Berlin, in press.

CCE 32: Dudgeon, S., Wagner, A., Vaisnys, J. R. & L. W. Buss (1995). Dynamics of gastrovascula circulation in the colonial hydroid, Podocoryne carnea. The one-polyp case. J. Exp. Biol. submitted.

CCE 34: Schmitz, O. J., Beckerman, A. P. & S. Litman (1995). The trophic dynamic consequences of adaptive foraging by herbivores. Evolutionary Ecology submitted.

CCE 35: Johnston, K. M. & O. J. Schmitz (1995). Influence of climate change on the distribution of selected wildlife species within the continental USA. Ecological Applications submitted.

CCE 36: Beckerman, A. P. (1995). Body size dependent patterns in functional responses: the evolutionary ecological basis for pattern in dynamics of ecological systems. Evolutionary Ecology submitted.

CCE 37: Freund, H. (1995). Self-maintaining lambda-organized and analysis via rewrite systems. Evolutionary Ecology submitted.

CCE 39: Laubichler, M. D. (1995). Wittgensteinian Biology. I. Rauch (ed.) Proceedings of the fifth Congress of the International Association for Semiotic Studies, Berkeley, Mouton de Gryter, Berlin, in press.

CCE 40: Rannala, B., Brown, C.R., & M.B. Brown (1996). Spatio-temporal refugia and parasitic avoidance in the Cliff Swallow. Ecology in press.

CCE 41: Fontana, W. and L.W. Buss (1996). The barrier of objects: From Dynamical Systems to bounded organizations. In J. Gasti and A. Karlquist, eds. Boundaries and Barriers. Addison-Wesley, Reading, Massachusetts.

Center For ECOSAVE
CE 1: Vrba, E. S. (1993). Turnover-pulses, the Red Queen, and related topics. American J. of Science 293A: 418-452.

CE 2: Clark, J. D., deHeinzelin, J., Schick, K., Hart, W. K., White, T. D., WoldeGabriel, G., Walter, R. C., Suwa, G., Asfaw, B., Vrba, E. S. & Y. H. Selassie (1994). Ages and young Oldowan asemblages in the Middle Awash Valley, Ethiopia. Science 264: 1907-1910.

CE 3: Vrba, E. S. (1994). An hypothesis of heterochrony in response to climatic cooling and its relevance to early hominid evolution. In R. Ciochon & R. Corruccini (ed.) Integrative paths to the past: Paleoanthropological advances in honor of F. Clark Howell. Prentice Hall, Englewood Cliffs, New Jersey. 345-376.

CE 4: Vrba, E. S. (1994). Possible turnover-pulses in antelope and hominid evolution. In E. S. Vrba, G. H. Denton, T. C. Partridge, & L. H. Burckle (ed.) Paleoclimate and evolution with emphasis on human origins. Yale University Press, New Haven, CT. in press.

CE 6: Vrba, E. S. & J. E. Gatesy (1994). New fossils of hippotragine antelopes from the Middle Awash deposits, Ethiopia, in the context of a phylogenetic analysis of hippotragini (Bovidae, Mammalia). Palaeontologia Africana in press.

CE 7: Gatesy, J., Hayachi, S., Vrba, E. S. & R. DeSalle (1994). Correlated character change and rate estimations for rRNA stem regions. In preparation.

CE 8: Vrba, E. S., Vaisnys, J. R., Gatesy, J. E., DeSalle, R., & K. Y. Wei (1994). Analysis of paedomorphosis using allometric characters: The example of reduncici antelopes (Bovidae, Mammalia). Syst. Biol. 43 (1): 92-116.

CE 9: Vrba, E. S. & J. Gatesy (1994). New Antelope Fossils from Awash, Ethiopia, and Phylocenetic analysis of Hippotragini (Bovidae, Mammalia). Palaeontological Africana 31 (0): 55-72.

CE 10: Vrba, E. S. (1994). An hypothesis of early hominid heterochrony in response to climatic cooling. In R. Ciochon and R. Corruccini (eds), Integrative Paths to the Past: Paleoanthro-pological Advances in Honour of F. Clark Howell, pp. 345-376. Prentice Hall, New York.

CE 11: Gatesy, J., Hayachi, S., DeSalle, R. & E. S.Vrba (1994). Rate limits for mispairing and compensatory change: the mitochrondrial ribosomal DNA of antelopes. Evolution 48 (1): 188-196.

CE 12: Vrba, E. S. (1995). Species as habitat specific, complex systems. In J. C. Masters, D. M. Lambert and H. G. Spencer (ed.) The Recognition of Species: Speciation and the Recognition concept, pp. 3-44. Johns Hopkins University Press. Washington, DC.

CE 13: Lieberman, B. & E. S. Vrba (1994). Levels of selection. Bioscience. 45 (6) 394-399.

CE 14: Clark, J.D., De Heinzelin, J., Schick, K., Hart, W., White, T., WoldeGabriel, R. W., Suwa, G., Asfaw, B., Vrba, E.S. & Y. Haile-Selassie (1994). Middle Pleistocene discoveries in the Middle Awash Valley Ethiopia. Science 264:1907-10.

Center For Earth Observation
CEO 1: Fraser, R., Warrent, M. & P. Barten (1995). Comparative evaluation of land cover data sources for erosion prediction. Water Resources Bulletin in press.

Center For Global Change
CGC 1: Pegram, W. J., Krishnaswami, D., Ravizza, G. E. & K. K. Turekian (1992). The record of sea water 187Os/186Os variation through the cenozoic. Earth and Planetary Science Letters 113: 569-576.

CGC 2: Turekian, K. K. & N. Tanaka (1992). The use of atmospheric cosmogenic 35S and 7Be in determining depositional fluxes of SO2. Geophysical Res. Letters 19 (17): 1767-1770.

CGC 3: Tanaka, N. & K. K. Turekian (1995). The determination of the dry deposition flux of SO2 using cosmogenic 35S and 7Be measurements. J. Geophys. Res. 100: 2841-2848.

CGC 4: Pegram, W. J., Esser, B. K., Krishnaswami, S., & K. K. Turekian (1994). The isotopic composition of leachable osmium from river sediments. Earth and Planetary Let. in press.

CGC 5: Turekian, K. K., Tanaka, N., Turekian, V. C., Torgersen, T. & E. C. DeAngelo (1995). Transfer rates of dissolved tracers through estuaries based on 228 Ra: A study of Long Island Sound. Cont. Shelf Res. in press.

CGC 6: Prospero, J. M., Schmitt, R., Cuevas, E., Savoie, D., Graustein, W. C., Turekian, K. K., Volz-Thomas, A. A., Diaz, A., Oltmans, S. & H. Levy (1995). Temporal variability of summer-time ozone and aerosols in the free troposphere over the eastern North Atlantic. Geophys. Res. Let. in press.

CGC 7: Turekian, K. K., Krishnaswami, S., Ribe, N. M. & I. M. Reinitz (1995). Radioactive disequilibrium among 238U series nuclides in recent volcanic rocks: a model for chronology and mechanism of formation. (Vinogradov Jubilee Volume) Nauka Publishing House, Moscow, in press.

Center For Human Ecology, Environmental and Infectious Disease
CHD a: Montagnini, F., Singer, B., Auer, B. & N. Muñiz-Miret (Spring 1993). TRI Initiative-Human health and effective utilization of tropical forests. TRI News-Journal of Tropical Resource Institute, Yale University School of Forestry and Environmental Studies 12(1): 1-2.

CHD 1: Land Use and Health in the Amazon: An Update of the Project's Second Year. TRI News, Spring 1995.

CHD 2: Montagnini, F. & N. Muñiz-Miret (August 3, 1995). Vegetation and soils of tidal floodplains of the Amazon estuary: A comparison of várzea andterra firme forest in Pará, Brazil. Journal of Tropical Ecology submitted.

CHD 3: Muñiz-Miret, N., Vamos, R., Hiraoka, M., Montagnini, F. & R. Mendelsohn (1995). The Economic Value of Managing Açaí (Euterpe oleracea Maart) in the floodplains of the Amazon Estuary, Pará, Brazil. Journal Ecological Economics submitted.