2008 Fall Publications from the Department of Ecology and Evolution

• Keith, D.A, H.R. Akcakaya, W. Thuiller, G.F. Midgley, R.G. Pearson, S.J. Phillips, H.M. Regan, M.B. Araujo, T.G. Rebelo. 2008. Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models. Biology Letters 4:560-563.
• Mace, G.M., N. Collar, K.J. Gaston, C. Hilton-Taylor, H.R. Akcakaya, N. Leader-Williams, E.J. Milner-Gulland and S.N. Stuart. 2008. Quantification of extinction risk: IUCN's system for classifying threatened species. Conservation Biology 22:1424-1442.
• Akcakaya, H.R. and B.W. Brook. 2008. Methods for determining viability of wildlife populations in large landscapes. Pages 449-471 in: Models for Planning Wildlife Conservation in Large Landscapes. J.J. Millspaugh and F.R. Thompson, III (editors). Elsevier/Academic Press, Burlington, MA.
• Akcakaya, H.R., J. D. Stark, and T. S. Bridges (editors). 2008. Demographic Toxicity: Methods in Ecological Risk Assessment. Oxford University Press, New York.
• ABaillie, J.E.M., B. Collen, R. Amin, H.R. Akcakaya, S.H.M. Butchart, N. Brummitt, T.R. Meagher, M. Ram, C. Hilton-Taylor, and G.M. Mace. 2008. Towards monitoring global biodiversity. Conservation Letters 1:18-26.
• Nomakuchi, S., P. J. Park, and M. A. Bell. Correlation between exploration activity and use of social information in threespine sticklebacks. Behavioral Ecology. In press.
• Aguirre, W. E., K. E. Ellis, M. Kusenda, and M. A. Bell. 2008. Phenotypic variation and sexual dimorphism in anadromous threespine stickleback: implications for postglacial adaptive radiation. Biological Journal of the Linnean Society. 95:465-478.
• Hunt, G., M. A. Bell, and M.P. Travis. 2008. Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage. Evolution 62:700-710. (doi:10:1111/j.1558-5646.2007.00310.x)
• Arif, S., W. E. Aguirre, and M. A. Bell. Evolutionary diversification of operculum shape in Cook Inlet threespine stickleback. Biol. J. Linn. Soc. In press.
• Bell, M. A., J. D. Stewart and P. J. Park. The world’s oldest fossil threespine stickleback. Copeia. In press.
• Dávalos, L.M., A. C. Bejarano, and H. L. Correa. 2008. Disabusing cocaine: Pervasive myths and enduring realities of a globalised commodity. International Journal of Drug Policy.
• Dávalos, L.M., and A. Corthals. 2008. A new species of Lonchophylla (Chiroptera: Phyllostomidae) from the eastern Andes of northwestern South America. American Museum Novitates 3635, 1-16.
• Stoebel, D. M., A. M.Dean, D.E. Dykhuizen. 2008. The cost of expression of Escherichia coli lac operon proteins is in the process, not the products. Genetics 178:1653-1660.
• Dykhuizen, D. E., D. Brisson, S. Sandigursky, G. P. Wormser, J. Nowakowski, R. B. Nadelman, and I. Schwartz. 2008. The propensity of different Borrelia burgdorferi sensu stricto genotypes to cause disseminated infections in humans. Am. J. Tropical Med Hygiene 78:806-810.
• Catherine H. Graham and Paul V. A. Fine. 2008. Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecology Lteers, 11:1265-1277.
• J. Gurevitch, T.G. Howard, I.W. Ashton, E.A. Leger, K.M. Howe, E. Woo and M. Lerdau. 2008. Effects of experimental manipulation of light and nutrients on establishment of seedlings of native and invasive woody species in Long Island, NY forests. Biological Invasions 10: 821-831.
• Lachance, J. 2008. A Fundamental Relationship Between Genotype Frequencies and Fitnesses Genetics 180:1087-93
• Levinton, J.S. 2008. The Cambrian Explosion: How Do We Use the Evidence? BioScience 58: 855-864
• Levinton, J.S., Pochron, S.T. 2008. Temporal and geographic trends in mercury concentrations in muscle tissue in five species of Hudson Rive, USA, fish. Envrionmental Toxicology and Chemistry. 27: 1691-97.
• Bossdorf, O., C. Richards and M. Pigliucci. 2008. Epigenetics for ecologists. Ecology Letters 11: 106-115.
• Pigliucci, M. 2008. The borderlands between science and philosophy: an introduction. Quarterly Review of Biology 83(1): 7-15.
• Pigliucci, M. 2008. Is evolvability evolvable? Nature Reviews Genetics 9: 75-82.
• Pigliucci, M. Okasha's Evolution and the Levels of Selection: toward a broader conception of evolutionary biology. Biology & Philosophy. In press.
• Pigliucci, M. Sewall Wright's adaptive landscapes: 1932 vs. 1988. Biology & Philosophy. In press.
• Pigliucci, M. What, if anything, is an evolutionary novelty? Philosophy of Science. In press.
• Richards, C., R. L. Walls, J. P. Bailey, R. Parameswaran, T. George and M. Pigliucci. 2008. Plasticity in salt tolerance traits allows for invasion of novel habitat by Japanese Knotweed s.l. (Fallopia japonica and F. x bohemica, Polygonaceae). American Journal of Botany 95(8): 931-942.
• Bossdorf, O. and M. Pigliucci. Plasticity to wind is modular and genetically variable in Arabidopsis thaliana. Evolutionary Ecology. In press.
• Przeslawski R., Bourdeau P.E., Doall M.H.,, Pan J., Perino L., Padilla D.K. 2008. The effects of a harmful alga on bivalve larval lipid stores. Harmful Algae 7:802-807.
• Perino L.L., Padilla D.K., Doall M.H. 2008. Testing the accuracy of morphological identification of northern quahog larvae. Journal of Shellfish Research 27:1081-1085.
• Doall, M.H., Padilla, D.K., Lobue, C.P., Clapp, C., Webb, A.R., Hornstein, J. 2008. Evaluating northern quahog (= hard clam, Mercenaria mercenaria L.) restoration: are transplanted clams spawning and reconditioning? Journal of Shellfish Research 27(5):1069-1080.
• M.E. Bradley, J.S. Rest, W.H. Li, and N.B. Schwartz. Sulfate Activation Enzymes: Phylogeny and Association with Pyrophosphatase. J. Mol. Evol. (2008).
• Amaral, Ana R., M. Manuela Coelho, Jesús Marugán-Lobón and F. James Rohlf. 2008. Geometric morphometric analysis of cranial shape in closely related delphinid cetacean species: an evolutionary approach: Evolutionary morphology the skull in delphinids on the basis of geometric morphometric procedures. Zoology, 112:38-47.
• Harcourt-Smith, W. H. E., M. Tallman, S. R. Frost, D. F. Wiley, F. J. Rohlf, E. Delson. 2008. Analysis of selected hominoid joint surfaces using laser scanning and geometric morphometrics: a preliminary report. Pp.373-383 in E. J. Sargis and M. Dagosto (eds.) Mammalian Evolutionary Morphology: A Tribute to Frederick S. Szalay. Springer: Dordrecht.
• Valentin, A. E., X. Penin, J.-P. Chanut, J.-M. Sévigny, and F. J. Rohlf. 2008. Arching effect on fish body shape in geometric morphometric studies. J. of Fish Biology, 73:623-638.
• Jeong, S., Rebeiz. M., Andolfatto, P., Werner, T., True, J.R., and Carroll, S.B. 2008. The evolution of gene regulation underlies the morphological divergence of two closely related Drosophila species. Cell 132: 783-703.
• True, J.R. 2008. Combing evolution. Evol Dev. 10:400-402.
• Yukilevich, R. and J.R. True. 2008. African morphology, behavior and phermones underline incipient sexual isolation between US and Caribbean Drosophila melanogaster. Evolution 62: 2807-2828.
• Yukilevich, R., Lachance, J., Aoki, F., True, J. R. 2008 Long-term evolution of epistatic genetic networks. Evolution 62:2215-2235.
• Yukilevich R, True J.R. 2008 Incipient sexual isolation among cosmopolitan Drosophila melanogaster populations. Evolution 62:2112-21.

2008 Spring Publications from the Department of Ecology and Evolution

• Akçakaya, H.R., G. Mills, and C. P. Doncaster. 2007. The role of metapopulations in conservation. Pages 64-84 in Key Topics in Conservation Biology. D.W. Macdonald and K. Service, editors. Blackwell.
• Akçakaya, H.R., S.H.M. Butchart, G.M. Mace, S.N. Stuart, and C. Hilton-Taylor. 2006. Use and misuse of the IUCN Red List Criteria in projecting climate change impacts on biodiversity. Global Change Biology 12:2037-2043.
• Butchart, S., H.R. Akçakaya, J. Chanson, J.E.M. Baillie, B. Collen, S. Quader, W. R. Turner, R. Amin, S.N. Stuart, C. Hilton-Taylor. 2007. Improvements to the Red List Index. PLoS ONE 2(1): e140. doi:10.1371/journal.pone.0000140.
• Butchart, S., H.R. Akçakaya, E. Kennedy, L. Master and C. Hilton-Taylor. 2006. Biodiversity indicators based on trends in conservation status: strengths of the IUCN Red List Index. Conservation Biology 20:579–581.
• Dunham, A.E., H.R. Akçakaya, T. S. Bridges. 2006. Using scalar models for precautionary assessments of threatened species. Conservation Biology 20: 1499-1506.
• Radeloff, V.C., D.J. Mladenoff, E.J. Gustafson, R.M. Scheller, H.S. He, P.A. Zollner, H.S He, and H.R. Akçakaya. 2006. Modeling forest harvesting effects on landscape pattern in the Northwest Wisconsin Pine Barrens. Forest Ecology and Management 236: 113-126.
• Reed, J.M., H.R. Akçakaya, M. Burgman, D. Bender, S.R. Beissinger, and J.M. Scott. 2006. Critical habitat. Pages 164-177 in The Endangered Species Act at Thirty: Conserving Biodiversity in Human-dominated Landscapes (volume 2). J.M. Scott, D.D. Goble, and F.W. Davis, editors. Island Press, Washington.
• Banta, J. A., S. C. Stark, M. H. H. Stevens, T. H. Pendergast, A. Baumert, and W. P. Carson. 2008. Light reduction predicts widespread patterns of dominance between asters and goldenrods. Plant Ecology: DOI:10.1007/s11258-11008-19412-11253.
• Bossdorf, O., C. Richards, et al. 2008. Epigenetics for ecologists. Ecology Letters 11:106-115.
• Dávalos LM, Perkins SL. 2008. Saturation and base composition bias explain phylogenomic conflict in Plasmodium. Genomics. 2008 May;91(5):433-42. Epub 2008 Mar 4.
• Dustin Brisson, Daniel E. Dykhuizen and Richard S. Ostfeld. 2008. Conspicuous impacts of inconspicuous hosts on the Lyme disease epidemic. Proc. R. Soc. B (2008) 275, 227–235, doi:10.1098/rspb.2007.1208.
• Evgeni V. Sokurenko, Richard Gomulkiewicz and Daniel E. Dykhuizen. 2006. Source–sink dynamics of virulence evolution. NATURE REVIEWS, MICROBIOLOGY, 548-555, Vol.4, July 2006.
• Natalia Korotkova, Sujay Chattopadhyay, Tami A. Tabata, Viktoria Beskhlebnaya, Vladimir Vigdorovich, Brett K. Kaiser, Roland K. Strong, Daniel E. Dykhuizen, Evgeni V. Sokurenko and Steve L. Moseley. 2007. Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli. Molecular Microbiology (2007) 64(1), 180–194 doi:10.1111/j.1365-2958.2007.05648.x.
• Sujay Chattopadhyay, Michael Feldgarden, Scott J. Weissman, Daniel E. Dykhuizen, Gerald van Belle, Evgeni V. Sokurenko. 2007. Haplotype Diversity in "Source-Sink" Dynamics of Escherichia coli Urovirulence. J. Mol. Evol. (2007) 64:204–214, DOI: 10.1007/s00239-006-0063-5.
• Sujay Chattopadhyay, Daniel E. Dykhuizen, Evgeni V. Sokurenko. 2007. ZPS: visualization of recent adaptive evolution of proteins. BMC Bioinformatics 2007, 8:187 doi:10.1186/1471-2105-8-187.
• Byun-McKay, S. A. and Geeta, R. 2007. Protein subcellular relocalization: a new perspective on the origin of novel genes. Trends Ecol. Evol. 22:338-344.
• Champagne, C.E.M., Goliber, T. E., Wojciechowski, M. F., Mei, R. W., Townsley, B. T., Wang, K., Paz M. W., Geeta, R., and Neelima R. Sinha. 2007. Compound Leaf Development and Evolution in the Legumes. Plant Cell 19 3369-3378.
• Geeta, R. and Gharaibeh, W. 2007. Historical evidence for a pre-Columbian presence of Datura in the Old World and implications for a first millenium transfer from the New World. J. Biosci. 32: 1227-1244.
• Tellez, V.O. and Geeta, R. (in press). Dioscorea howardiana, a new species in section Trigonobasis (Dioscoreaceae). Brittonia.
• Tellez, V.O. and Geeta, R. (accepted). Sinopsis taxonómica de la sección Apodostemon (Dioscorea; Dioscoreaceae). Revista Mexicana de Biodiversidad.
• Ginzburg, L.R. and Damuth, J. 2008. The space-lifetime hypothesis: viewing organisms in four dimension, literally. American Naturalist 171:125-131.
• Ginzburg, L.R., and Jensen, C.XJ. 2008. From controversy to consensus: the indirect interference functional response. SIL Biology 30/2, April 2008.
• Ginzburg, L.R., Jensen, CX. J. and Yule, J.V. 2007. Aiming the "unreasonable effectiveness of mathematics" at ecological theory. Ecological Modeling 207, pp.356-362.
• Ginzburg, L.R. and Colyvan, M. 2004. Ecological Orbits: how planets move and populations grow. Oxford University Press, New York, NY.
• Jensen, C, Jeschke, J.M. and Ginzburg, L.R. 2007. A direct, experimental test of resource vs. consumer dependence: comment. Ecology 88(6), pp.1600-1602.
• Jensen, C. X., and Ginzburg, L. R. 2005. Paradoxes or theoretical failures? The jury is still out. Ecological Modeling. 118 (2005):3-14.
• N. Mouquet, T. Daufresne, S. M. Gray and T. E. Miller. 2008. Modelling the relationship between a pitcher plant (Sarracenia purpurea) and its phytotelma community: mutualism or parasitism? Functional Ecology 22:728-737.
• Hoch, JM. 2008. Variation in penis morphology and mating ability in the barnacle, Semibalanus balanoides. Journal of Experimental Marine Biology and Ecology, 359 pp.126-130. 9 May 2008.
• Levinton, J.S., Pochron, S. 2008. Temporal and geographic trends in mercury concentrations in muscle tissue in five species of Hudson River, USA, fish. Environmental Toxicology and Chemistry. 27:1691-1697.
• Norris Z. Muth and Massimo Pigliucci, 2007. Implementation of a novel framework for assessing species plasticity in biological invasions: responses of Centaurea and Crepis to phosphorus and water availability. Journal of Ecology 95:1001-1013.
• Pigliucci, M. 2008. The borderlands between science and philosophy: an introduction. Quarterly Review of Biology 83(1):7-15.
• Pigliucci, M. 2008. Is evolvability evolvable? Nature Reviews Genetics 9:75-82.
• Pigliucci, M. 2007. Do we need an extended evolutionary synthesis? Evolution 61(12):2743-2749.
• Pigliucci, M. 2007. Finding the way in phenotypic space: the origin and maintenance of constraints on organismal form. Annals of Botany 100:433-438.
• Banta, J. A., J. Dole, M. B. Cruzan, and M. Pigliucci. 2007. Evidence of local adaptation to coarse-grained environmental variation in Arabidopsis thaliana. Evolution 61(10):2419-2432.
• Harcourt-Smith, W. H. E., M. Tallman, S. R. Frost, D. F. Wiley, F. J. Rohlf, E. Delson. 2008 (In press). Analysis of selected hominoid joint surfaces using laser scanning and geometric morphometrics: a preliminary report. Pp.000-000 in E. J. Sargis and M. Dagosto (eds.) Mammalian Evolutionary Morphology: A Tribute to Frederick S. Szalay. Springer: Dordrecht.
• Amaral, Ana R., M. Manuela Coelho, Jesús Marugán-Lobón and F. James Rohlf. 2008 (in press). Geometric morphometric analysis of cranial shape in closely related delphinid cetacean species: an evolutionary approach: Evolutionary morphology the skull in delphinids on the basis of geometric morphometric procedures. Zoology.
• Antonyshyn , O. M., J. G. Mainprize, F. J. Rohlf, and M. A. Pahuta 2008 (in press). Biometric Morphing: a novel technique for the analysis of morphological outcomes following facial surgery. Annals of Plastic Surgery.
• J. Khai Tran, Tiina Ylioja, Ronald F. Billings, Jacques Régnière, and Matthew P. Ayres. 2007. IMPACT OF MINIMUM WINTER TEMPERATURES ON THE POPULATION DYNAMICS OF DENDROCTONUS FRONTALIS. Ecological Applications, 17(3), 2007, pp.882–899.