2012 Fall Publications from the Department of Ecology and Evolution

• Akçakaya, H.R., S. Ferson, M.A. Burgman, D.A. Keith, G.M. Mace and C.R. Todd. 2012. Commentary: IUCN classifications under uncertainty. Environmental Modelling & Software. 38:119-121.
• Harris, J.B.C., D.A. Fordham, P.A. Mooney, L.P. Pedler, M.B. Araújo, D.C. Paton, M.G. Stead, M.J. Watts, H.R. Akçakaya, and B.W. Brook. 2012. Managing the long-term persistence of a rare cockatoo under climate change. Journal of Applied Ecology. 49:785–794.
• Furan, C. G., F. A. von Hippel, and M. A. Bell. 2012. Partial reproductive isolation of a recently derived resident-freshwater population of threespine stickleback (Gasterosteus aculeatus) from its putative anadromous ancestor. Evolution 66
• Blass, E., M. Bell, and S. Boissinot. 2012. Accumulation and rapid decay of non-Ltr retrotransposons in the genome of the threespine stickleback. Genome Biology and Evolution 4:687-702. (DOI:10.1093/gbe/evs044)
• Lohman, B. K, H. I. Sirotkin, and M. A. Bell. 2012. A whole-mount method for trypsin clearing and collagen type II antibody staining. Copeia. In press.
• Dávalos, L.M.*, A.L. Cirranello*, J.H. Geisler, and N.B. Simmons. 2012. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biological Reviews 84(7). *Equally authored.
• Corthals, A., A. Köller, D.W. Martin, R. Rieger, E.I. Chen, M. Bernaski, G. Recagno, and L.M. Dávalos. 2012. Detecting the Immune System Response of a 500 Year-Old Inca Mummy. PLoS One 7(7), e41244.
• Hutter CR & Guayasamin JM. 2012. A new cryptic species of Glassfrog (Centrolenidae: Nymphargus) from Reserva Las Gralarias, Ecuador. Zootaxa, 3257: 1–21.
• Coloma LA, Carvajal-Endara S, Dueñas JF, Paredes-Recalde A, Morales-Mite M, Almeida-Reinoso D, Tapia EE, Hutter CR, Toral E, & Guayasamin JM. 2012. Molecular phylogenetic systematics of stream frogs of the Hyloscirtus larinopygion group (Anura: Hylidae), and description of two new species from Ecuador. Zootaxa, 3364: 1–74.
• Arditi, R and Ginzburg, L.R. 2012. How Species Interact: Altering the Standard View on Trophic Ecology. Oxford University Press, New York, NY.
• Coylyvan, M, and Ginzburg, L.R. 2012. Ecological laws. In Oxford Bibliographies Online: Ecology. Ed. David Gibson: Oxford University Press, New York.
• Jorge Velásquez-Tibatá, Paul Salaman, Catherine H. Graham. 2012. Effects of climate change on species distribution, community structure, and conservation of birds in protected areas in Colombia. Reg Environ Change, DOI:10.1007/s10113-012-0329-y.
• Lopez, G.R., Levinton, J. 2012. Particulate organic detritus and detritus feeders in coastal food webs. Treatise on Estuarine and Coastal Science, volume 6, Trophic Structure of Estuaries and Coasts, Luczkovich, J., Wilson, J., eds., Elsevier, Amsterdam.
• Allen, B. J., Rodgers, B., Tuan, Y., Levinton, J. S. 2012. Size-dependent temperature and desiccation constraints on performance capacity: Implications for sexual selection in a fiddler crab. Journal of Experimental Marine Biology and Ecology 438:93-99.
• Munguia, P., Levinton, J.S., Silbiger, N.J. 2013. Latitudinal differences in thermoregulatory color change in Uca pugilator. Journal of Experimental Marine Biology and Ecology 440:8-14.
• Grant, E.H.C., H.J. Lynch, R. Muneepeerakul, M. Arunachalam, I. Rodriguez-Iturbe, and W.F. Fagan. 2012. Interbasin water transfer, riverine connectivity, and spatial controls on fish biodiversity. PLoS ONE. 7(3):e34170.
• Lynch, H.J., R. Naveen, P.N. Trathan and W.F. Fagan. 2012. Spatially integrated assessment reveals widespread changes in penguin populations on the Antarctic Peninsula. Ecology. 93(6):1367-1377.
• Casanovas, P., H.J. Lynch, and W.F. Fagan. 2012. Multi-scale patterns of lichen and moss richness along the Antarctic Peninsula. Ecography. 35:001-011.
• Lynch, H.J., R. White, A.D. Black, and R. Naveen. 2012. Detection, differentiation, and abundance estimation of penguin species by high-resolution satellite imagery. Polar Biology. 35:963-968.
• Lynch, H.J., W.F. Fagan, R. Naveen, S.G. Trivelpiece, and W.Z. Trivelpiece. 2012. Differential advancement of breeding phenology in response to climate may alter staggered breeding among sympatric pygoscelid penguins. Marine Ecology Progress Series. 454:135-145.
• Rest, J.S., K. Bullaughey, G.P. Morris, W.H. Li. 2012. Contribution of Transcription Factor Binding Site Motif Variants to Condition-Specific Gene Expression Patterns in Budding Yeast. PLoS ONE. 7(2): e32274. doi:10.1371/journal.pone.003227.
• Xi, Z., R.K. Bradley, K.J. Wurdack, K.M. Wong, M. Sugumaran, K. Bomblies, J.S. Rest*, C.C. Davis. 2012. Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics, 13:227 doi:10.1186/1471-2164-13-227. *Co-corresponding author
• Zhang, T. , R. A. DeSimone, X. Jiao, F. J. Rohlf, W. Zhu, Q. Q. Gong, S. R. Hunt, T. Dassopoulos, R. D. Newberry, E. Sodergren, G. Weinstock, D. N. Frank, E. Li. 2012. Host genes related to Paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. PLoS ONE, 7(6):e30044. 7pp.
• Li, E., C. M. Hamm, A. Gulati, R. B. Sartor, H. Chen, X. Wu, T. Zhang, F. J. Rohlf, W. Zhu, C. Gu, C. E. Robertson, N. R. Pace, E. C. Boedeker, N. Harpaz, J. Yuan, G. M. Weinstock, E. Sodergren, D. N. Frank. 2012. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS ONE, 7(6):e26284. 10pp.
• Baab, K. L., K. P. McNulty, and F. J. Rohlf. 2012. The Shape of Human Evolution: A Geometric Morphometrics Perspective. Evolutionary Anthropology, 21:151-165.
• Cruz, R. A. L., M. J. R. Pante, and F. J. Rohlf. 2012. Geometric Analysis of Shell Shape Variation in Conus (Gastropoda: Conidae). Zoological Journal of the Linnean Society, 165:296-310.
• Fredric V. Vencl and Robert B. Srygley. 2012. Enemy targeting, trade-offs, and the evolutionary assembly of a tortoise beetle defense arsenal. Evol Ecol, DOI:10.1007/s10682-012-9603-1.
• Wiens JJ, Hutter CR, Mulcahy DG, Noonan BP, Townsend TM, Sites JM Jr, & Reeder TW. 2012. Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters, in press, published online: DOI:10.1098/rsbl.2012.0703.

2012 Spring Publications from the Department of Ecology and Evolution

• Aiello-Lammens, M.E., M.L. Chu-Agor, M. Convertino, R.A. Fischer, I. Linkov, and H.R. Akçakaya. 2011. The impact of sea-level rise on snowy plovers in Florida: Integrating geomorphological, habitat, and metapopulation models. Global Change Biology 17: 3644-3654.
• Chu-Agor, M.L., R. Muñoz-Carpena, G.A. Kiker, M.E. Aiello-Lammens, H.R. Akçakaya, M. Convertino, and I. Linkov. 2012. Simulating the fate of Florida Snowy Plovers with sea-level rise: exploring research and management priorities with a global uncertainty and sensitivity analysis perspective. Ecological Modelling 224:33-47.
• Fordham, D.A., H.R. Akçakaya, M. Araújo, J. Elith, D. Keith, R. Pearson, T.D. Auld, C. Mellin, J.W. Morgan, T.J. Regan, M. Tozer, M.J. Watts, M. White, B. Wintle, C. Yates, and B.W. Brook. 2012. Plant extinction risks under climate change: are forecast range shifts alone a good indicator of species vulnerability to global warming? Global Change Biology 18:1357-1371.
• Akçakaya, H.R., G.M. Mace, K.J. Gaston, H. Regan, A. Punt, S.H.M. Butchart, D.A. Keith, U. Gärdenfors. 2011. The SAFE index is not safe. Frontiers in Ecology and the Environment 9:485-486.
• Kuemmerle, T., K. Perzanowski, H.R. Akçakaya, F. Beaudry, T.R. van Deelen, I. Parnikoza, P. Khoyetskyy, D.M. Waller, and V.C. Radeloff. 2011. Cost-effectiveness of different conservation strategies to establish a European bison metapopulation in the Carpathians. Journal of Applied Ecology 48:317-329.
• Stanton, J.C., R.G. Pearson, N. Horning, P. Ersts, and H.R. Akçakaya. 2012. Combining static and dynamic variables in species distribution models under climate change. Methods in Ecology and Evolution 3:349-357.
• Bell, M. A. 2012. Adaptive landscapes, evolution, and the fossil record. In E. Svensson and R. Calsbeek (eds), The adaptive landscape in evolutionary biology, pp. 243-256. Oxford University Press, Oxford.
• Johnston, I. A., B. K. Kristjansson, C. G. P. Paxton, V. L A. Vieiara, D.J. Macqueen, and M. A. Bell. 2012. Universal scaling rules predict evolutionary patterns of myogeneisis in species with indeterminate growth. Proceedings of the Royal Society B in press. (doi:10.1098/rspb.2011.2536)
• Dumont, E.R., L.M. Dávalos, A. Goldberg, S.E. Santana, K. Rex, and C.C. Voigt. 2012. Morphological innovation, diversification and the invasion of a new adaptive zone. Proceedings of the Royal Society B: Biological Sciences. *Joint first authors. Popular press coverage in io9 and Nature.
• Geeta, R., L.M. Dávalos, A. Levy, L. Bohs, M. Lavin, K. Mummenhoff, N. Sinha, M.F. Wojciechowski. 2012. Keeping it simple: Flowering plants tend to retain, and revert to, simple leaves. New Phytologist 193(2), 481-493.
• Fisher-Reid, M.C. and J.J. Wiens. 2011. What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evolutionary Biology 11:300.
• Starke, A., Levinton, J., Doall, M. 2011. Restoration potential of Crassostrea virginica to the Hudson River, USA: A Spatio-temporal modeling approach. J. Shellfish Res., 30(3):671-684.
• Hoch, J.M., and J.S. Levinton. 2012. Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles. Evolution, published on line, January 11, 2012 doi:10.1111/j.1558-5646.2011.01548.
• Levinton, J. S. (February 2012). Macroevolution: Overview. In: Encyclopedia of Life Sciences 2012, John Wiley & Sons, Ltd: Chichester [DOI:10.1002/9780470015902.a0001771.pub2]
• Albins, M. A. and P. J. Lyons. 2012. Invasive red lionfish Pterois volitans blow directed jets of water at prey fish. Marine Ecology Progress Series 448:1-5.
• Rest JS, Bullaughey K, Morris GP, 2012. Li W-H (2012) Contribution of Transcription Factor Binding Site Motif Variants to Condition-Specific Gene Expression Patterns in Budding Yeast. PLoS ONE 7(2): e32274. doi:10.1371/journal.pone.0032274.
• Rohlf, F. J. and R. R. Sokal. 2012. Statistical Tables, 4th ed. Freeman: New York. Xii+258 pp.
• Sibony, P., Kupersmith, M., Rohlf, F. J. 2011. Shape analysis of the peripapillary RPE layer in papilledema and ischemic optic neuropathy. Investigative Ophthalmology & Visual Science, 52:7987-7995.
• Santiago Salinas, Kestrel O. Perez, Tara A. Duffy, Stephen J. Sabatino, Lyndie A. Hice, Stephan B. Munch, and David O. Conover. 2012. The response of correlated traits following cessation of fishery-induced selection. Evolutionary Applications ISSN 1752-4571.
• Sokal, R. R. and F. J. Rohlf. 2012. Biometry, 4th ed. Freeman: New York. 937 pp.
• Vencl FV, Trillo PA & Geeta R. 2011. Functional interactions among tortoise beetle larval defenses reveal trait suites and escalation. Behav. Ecol. Sociobiol. 64(2):227-239.