Ecology & Evolution Department - Stony Brook University

Author: Arif, S., W. E. Aguirre, and M. A. Bell. 2009.
Title: Evolutionary diversification of operculum shape in Cook Inlet threespine stickleback.
Journal: Biol. J. Linn. Soc. 97:832-844.
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Author: Edwin H. Battley 2009.
Title: Is electron equivalence between substrate and product preferable to C-mol equivalence in representations of microbial anabolism applicable to "origin of life" environmental conditions?.
Journal: Journal of Theoretical Biology, 260 (2009) 267-275, doi:10.1016/j.jtbi.2009.05.032.
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Author: Bell, M. A., J. D. Stewart and P. J. Park. 2009.
Title: The world's oldest fossil threespine stickleback.
Journal: Copeia 2009:256-265.
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Author: Bell, M. A. 2009.
Title: I. 17. Microevolution. In: S. A. Levin (ed.).
Journal: The Princeton Guide to Ecology, pp. 126-133, Princeton University Press, Princeton.
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Author: Bell, M. A. 2009.
Title: Implications of fossil threespine stickleback for Darwinian gradualism.
Journal: Journal of Fish Biology. (in press).
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Author: Brook, B.W., H.R. Akçakaya, D.A. Keith, G.M. Mace, R.G. Pearson, and M.B. Araujo. 2009.
Title: Integrating bioclimate with population models to improve forecasts of species extinctions under climate change.
Journal: Biology Letters 5:723-725.
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The results of facial surgery are intuitively judged in terms of the visible changes in facial features or proportions. However, describing these morphologic outcomes objectively remains a challenge. Biometric morphing addresses this issue by merging statistical shape analysis and image processing. This study describes the implementation of biometric morphing in describing the average morphologic result of facial surgery. The biometric morphing protocol was applied to pre- and postoperative images of the following: (1) 40 dorsal hump reduction rhinoplasties and (2) 20 unilateral enophthalmos repairs. Preand postoperative average images (average morphs) were generated. The average morphs provided an objective rendering of nasal and periorbital morphology, which summarized the average features and extent of deformity in a population of patients. Subtle alterations in morphology after surgery, which would otherwise be difficult to identify or demonstrate, were clearly illustrated. Biometric morphing is an effective instrument for describing average facial morphology in a population of patients.

Author: Burbrink, F.T., and R.A. Pyron. 2009.
Title: How does ecological opportunity influence rates of speciation, extinction, and morphological diversification in New World ratsnakes (tribe Lampropeltini)?
Journal: Evolution (in press).
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Author: Burger, O. and Ginzburg, L.R. 2009.
Title: Of size and extinction: A random walk model predicts the body size of lowest risk for mammals.
Journal: Evolutionary Ecology Research. Evolutionary Ecology Research. 11:1017-1029.
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Author: Lyubov E. Burlakova, Alexander Y. Karatayev, Dianna K. Padilla, Leah D. Cartwright and David N. Hollas. 2009.
Title: Wetland restoration and invasive species: apple snail (Pomacea insularum) feeding on native and invasive aquatic plants.
Journal: Restoration Ecology 17:433-440.
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Author: Chattopadhyay, S., S. J. Weissman, V. N. Minin, T. A. Russo, D. E. Dykhuizen, E. V. Sokurenko. 2009.
Title: High Frequency of Hotspot Mutations in Core Genes of Escherichia coli due to Short-Term Positive Selection.
Journal: Proc. Natl. Acad. Sci. USA 106:12412-12417.
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Author: Chattopadhyay, S., R. N. Paranjpye, D. E. Dykhuizen, E. V. Sokurenko, M. S. Strom. 2009.
Title: Comparative evolutionary analysis of the major structural subunit of Vibrio vulnificus type IV pili.
Journal: Mol. Bio. Evol. 26:2185-2196.
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Author: Dávalos LM, Porzecanski AL. 2009.
Title: Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria.
Journal: Molecular Phylogenetics and Evolution. Oct;53(1):234-48. Epub 2009 Jun 11.
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Author: Dávalos LM, Bejarano AC, Correa HL. 2009.
Title: Disabusing cocaine: pervasive myths and enduring realities of a globalised commodity.
Journal: International Journal of Drug Policy. Sep;20(5):381-6. Epub 2008 Dec 2.
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Author: Dávalos, L.M. 2009.
Title: Earth history and the evolution of Caribbean bats.
Journal: Island bats: ecology, evolution, and conservation. Fleming, T.H., and P.A. Racey (eds.). Chicago: University of Chicago Press.
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Author: Dukes, J.S., J. Pontius, D. Orwig, J.R. Garnas, V.L. Rodgers, N.Brazee, B. Cooke, KA. Theoharides, E.E. Stange, R. Harrington, J. Ehrenfeld, J. Gurevitch, M. Lerdau, K. Stinson, R. Wick, and M. Ayres. 2009.
Title: Responses of insect pests, pathogens, and invasive plant species to climate change in the forests of northeastern North America: What can we predict?
Journal: Can. J. For. Res. 39:231-248.
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Author: Dykhuizen, D. E., A. M. Dean. 2009.
Title: Experimental Evolution from the bottom up.
Journal: In (T. Garland Jr, M. R. Rose, eds.) Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. University of California Press. Pp 67-87.
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Author: Dykhuizen, D. E., and I. N. Wang. 2009.
Title: Animal foraging meets viruses.
Journal: Evol. Ecol. Res.
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Author: Elith, J. and C.H. Graham. 2009.
Title: Do they / How do they / WHY do they differ? -- on finding reasons for differing performances of species distribution models.
Journal: Ecography, 32:66-77. (Invited opinion paper).
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Author: Freile, F.J., J.L. Parra and C.H. Graham.
Title: Distribution and conservation of Grallaria and Grallaricula antpittas (Formicariidae) in Ecuador.
Journal: Bird Conservation International (in press).
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Author: Futuyma, D. J. 2009.
Title: Evolution, second edition.
Journal: Sinauer, Sunderland, Mass.
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Author: Futuyma, D. J., and A. A. Agrawal. 2009.
Title: Evolutionary history and species interactions.
Journal: Proc. Nat. Acad. Sci. USA 106:18043-18044.
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Author: Futuyma, D. J., and A. A. Agrawal. 2009.
Title: Macroevolution and the biological diversity of plants and herbivores.
Journal: Proc. Nat. Acad. Sci. 106:18054-18061.
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Author: Futuyma, D. J., and A. F. Bennett. 2009.
Title: The importance of experimental studies in evolutionary biology.
Journal: Pp. 15-30 in T. Garland, Jr., and M. R. Rose (eds.), Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments. University of California Press, Berkeley.
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Author: Futuyma, D.J., and R.K. Colwell. 2009.
Title: Lawrence B. Slobodkin (1928-2009): Integrating theory, models, and experiments in ecology.
Journal: PLoS Biology. 7(12):1-2 (e1000261).
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Author: Ginzburg, L.R., Burger, O., and Damuth, J.,2009.
Title: The May threshold and life history allometry.
Journal: Ecology Letters (submitted).
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Author: Burger, O. and Ginzburg, L.R. 2009.
Title: Of size and extinction: A random walk model predicts the body size of lowest risk for mammals.
Journal: Evolutionary Ecology Research. 11:1017-1029.
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Author: Graham, C.H., J.L. Parra, C. Rahbek, J. A. McGuire. 2009.
Title: Phylogenetic structure in tropical hummingbird communities.
Journal: Proceedings of the National Academy of Sciences (in press).
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Author: Graham, C.H., B.A. Loiselle, J. Velasquez* and F. Cuesta.
Title: Species distribution modelling and the challenge of predicting future distributions. In. Forecasting how climate change will influence biological diversity.
Journal: Invited chapter for SCOPE book (in press).
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Author: Graham, C.H. and S. Goetz. 2009.
Title: GIS and remote sensing.
Journal: In Simon A. Levin (Ed.). The Princeton Guide to Ecology. Princeton University Press.
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Author: Gurevitch, J. and K. Mengersen. 2009.
Title: A statistical view of research synthesis of patterns of species richness along productivity gradients: devils, forests and trees.
Journal: Ecology (in press).
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Author: Gurevitch, J. 2009.
Title: Invasions and plant competition. In: Encyclopedia of Invasive Introduced Species.
Journal: D. Simberloff and M. Rejmanek, eds. University of California Press, Berkeley CA. (in press).
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Author: Hickerson, MJ., B.C. Carstens, C. Cavender-Bares, K. Crandall, C. H. Graham, J. Johnson, L. Rissler, P.F. Victoriano, and B. Yoder.
Title: 20 years after Avise et al. 1987: Comparative phylogeography fulfilling original promise by integrating with emerging fields.
Journal: Molecular Evolution and Phylogenetics (in press).
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Author: Hsiao, H., M. Friess, B. Bradtmiller, and F. J. Rohlf. 2009.
Title: Development of sizing structure for fall arrest harness design.
Journal: Ergonomics, 52:1128-1143.
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Updated harness designs are needed to accommodate diverse populations in the current workforce. This paper determined an improved fall-arrest harness sizing scheme and strap-length configurations for harness design. A 3-D elliptic Fourier analysis (EFA) procedure with 123 coefficients was developed to quantify torso-shape effect on harness fit, based on 3-D data of 108 women and 108 men. The EFA coefficients were then applied to 600 representative body scans from a national database of 2382 participants to establish an improved sizing system. Study outcomes suggested a more upward back D-ring location for women than current unisex designs to accommodate female torso form and mitigate their fit problem. Results also suggested an improved system of three sizes for women and three sizes for men. New harness sizing charts for women and men were proposed accordingly. Using the most current 3-D whole-body digital scanning technology, this study assembled data from a US workforce to establish an improved fall-arrest harness sizing system and strap configurations for men and women. The information is useful for new generation harness designs to reduce the risk of worker injury.

Author: Alexander Y. Karatayev, Lyubov E. Burlakova and Dianna K. Padilla. 2009.
Title: Dreissena polymorpha in Belarus: history of spread, population biology, and ecosystem impacts.
Journal: In: The Zebra Mussels in Europe (G. van der Velde, S. Rajagopal and A. bij de Vaate, eds.).
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Author: Alexander Y. Karatayev, Lyubov E. Burlakova, Dianna K. Padilla, Sergey E Mastitsky and Sergej Olenin. 2009.
Title: Invaders are not a random selection of species.
Journal: Biological Invasions 11 SI:2009-2019.
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Author: Lachance J. 2009.
Title: Detecting selection-induced departures from Hardy-Weinberg proportions.
Journal: Genetics Selection Evolution 41:15.
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Viability selection influences the genotypic contexts of alleles and leads to quantifiable departures from Hardy-Weinberg proportions. One measure of these departures is Wright's inbreeding coefficient (F), where observed heterozygosity is compared with expected heterozygosity. Here, I extend population genetics theory to describe post-selection genotype frequencies in terms of post-selection allele frequencies and fitness dominance. The resulting equations correspond to non-equilibrium populations, allowing the following questions to be addressed: When selection is present, how large a sample size is needed to detect significant departures from Hardy-Weinberg? How do selection-induced departures from Hardy-Weinberg vary with allele frequencies and levels of fitness dominance? For realistic selection coefficients, large sample sizes are required and departures from Hardy-Weinberg proportions are small.

Author: Lachance J. 2009.
Title: Inbreeding, pedigree size, and the most recent common ancestor of humanity.
Journal: Journal of Theoretical Biology 261: 238-247.
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How many generations ago did the common ancestor of all present-day individuals live, and how does inbreeding affect this estimate? The number of ancestors within family trees determines the timing of the most recent common ancestor of humanity. However, mating is often non-random and inbreeding is ubiquitous in natural populations. Rates of pedigree growth are found for multiple types of inbreeding. This data is then combined with models of global population structure to estimate biparental coalescence times. When pedigrees for regular systems of mating are constructed, the growth rates of inbred populations contain Fibonacci n-step constants. The timing of the most recent common ancestor depends on global population structure, the mean rate of pedigree growth, mean fitness, and current population size. Inbreeding reduces the number of ancestors in a pedigree, pushing back global common ancestry times. These results are consistent with the remarkable findings of previous studies: all humanity shares common ancestry in the recent past.

Author: Lyons, P., C. Thornber, J. Portnoy, and E. Gwilliam.
Title: Dynamics of Macroalgal Blooms Along the Cape Cod National Seashore.
Journal: Northeast Naturalist.
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Accumulations of nuisance drift macroalgae along the open coast Atlantic beaches of the Cape Cod National Seashore have been observed on an anecdotal basis for over 50 years. This entire stretch of coastline is sandy, with no solid substrata for algal attachment. During the summer of 2006, we collected data on drift macroalgal accumulations repeatedly throughout this National Seashore. Peak biomass (consisting of several filamentous red species and green algae, primarily Ulva lactuca) was found in early August, mainly at the northernmost site. Our data, together with ocean current patterns and anecdotal evidence, suggest that macroalgae may originate in rocky shorelines of northern New England and are transported south by Gulf of Maine currents. Algae are most likely caught along the Cape Cod National Seashore shoreline by sand bars, particularly in the northern part of the shoreline.

Author: Moen, D. S., S. A. Smith, and J. J. Wiens. 2009.
Title: Community assembly through evolutionary diversification and dispersal in Middle American treefrogs.
Journal: Evolution 63:3228-3247.
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Author: Moritz, C., C. Hoskin, J. MacKenzie, B. L. Phillips, M. Tonione, N. Silva, J. VanDerWal, S. E. Williams, and C.H. Graham. 2009.
Title: Identification and dynamics of a cryptic suture zone in tropical rainforest.
Journal: Proceedings of the Royal Society, 276:1235-1244.
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Author: Nomakuchi, S., P. J. Park, and M. A. Bell. 2009.
Title: Correlation between exploration activity and use of social information in threespine sticklebacks.
Journal: Behavioral Ecology. 20:340-345.
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Author: Phillips, S., J. Elith, M. Dudik*, C.H. Graham, A. Lehmann, J. Leathwick and S. Ferrier. 2009.
Title: Sample selection bias and presence-only models of species distributions: implications for selection of background and pseudo-absences.
Journal: Ecological Applications, 19:181-197.
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Author: Pyron, R.A. 2009.
Title: A likelihood method for assessing molecular divergence time estimates and the placement of fossil calibrations.
Journal: Systematic Biology (in press).
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Author: Rodrigo Cogni & Douglas J. Futuyma.
Title: Local adaptation in a plant herbivore interaction depends on the spatial scale.
Journal: BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 97(3):494-502.
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Local adaptation has central importance in the understanding of co-evolution, maintenance of sexual reproduction, and speciation. We investigated local adaptation in the alkaloid-bearing legume Crotalaria pallida and its seed predator, the arctiid moth Utetheisa ornatrix, at different spatial scales. When we studied three populations from south-east Brazil (150 km apart), we did not find evidence of local adaptation, although we did find interpopulational differences in herbivore performance, and a significant interaction between herbivore sex and plant population. These results indicate that both moth and plant populations are differentiated at the regional scale. In a comparison of populations from Brazil and Florida, the herbivore showed local adaptation to its host plant; for both moth populations, the pupae were heavier when the larvae ate the sympatric than the allopatric host population. We discuss the scale dependence of our results and the possible causes for the lack of local adaptation at the regional scale, even in the presence of plant and moth differentiation. The results obtained demonstrate the importance of studying co-evolution and local adaptation at different geographical scales.

Author: Rodrigo Cogni
Title: Resistance to Plant Invasion? A Native Specialist Herbivore Shows Preference for and Higher Fitness on an Introduced Host.
Journal: BIOTROPICA DOI: 10.1111/j.1744-7429.2009.00570.x.
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The response of native herbivores to the introduction of a new plant to the community has important implications for plant invasion. Under the Enemy Release Hypothesis introduced species become invasive because of reduced enemy control in the new range, while under the New Association Hypothesis introduced species lack effective defenses against native enemies because they do not share an evolutionary history. I tested the response of a native South-American specialist herbivore Utetheisa ornatrix (Lepidoptera: Arctiidae) to a native (Crotalaria incana) and an introduced host (Crotalaria pallida) (Fabaceae: Papilionoideae). I compared seed predation rates between the two hosts in the field, and I tested preference and performance traits with common garden experiments. Utetheisa ornatrix caused much higher seed predation rates on the introduced host than on the native host. Females also preferred to oviposit on the introduced over the native host. Additionally, larvae feeding on the introduced host had higher fitness (higher pupal weight) than larvae feeding on the native host. I discuss how the response of this specialist herbivore to this introduced host plant contradicts the predictions of the Enemy Release Hypothesis and support the New Association Hypothesis. This study shows that the New Association Hypothesis can also be true for specialist herbivores.

Author: Kurt Schwenk, Dianna K. Padilla, George S. Bakken and Robert J. Full (shared first authorship). 2009.
Title: Grand challenges in organismal biology.
Journal: Integrative and Comparative Biology. 49:7-14.
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Author: Shapiro, M. D., B. R. Summers, S. Baldhadra, J. T. Aldenoven, A. L. Miller, C. B. Cunningham, M. A. Bell, and D. M. Kingsley. 2009.
Title: The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks.
Journal: Current Biology 19:1-6.
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Author: Thomassen, H.A., W. Buermann, B. Mila, C.H. Graham, S.E. Cameron, C.J. Schneider, J.P. Pollinger, S. Saatchi, R.K Wayne, T.B. Smith.
Title: Modeling environmentally associated morphological and genetic variation in a rainforest bird, and its application to conservation prioritization.
Journal: Evolutionary Applications (in press).
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Author: Tinoco, B.A., P.X. Astudillo, S.C. Latta and C.H. Graham. 2009.
Title: Distribution, ecology and conservation of an endangered Andean hummingbird: the violet-throated metaltail (Metallura baroni).
Journal: Bird Conservation International, 19:1-14.
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Author: VanDerWal, J., L.P. Shoo, C.H. Graham and S.E. Williams. 2009.
Title: Selecting pseudo-absence data for presence-only distribution modeling: how far should you stray from what you know?
Journal: Ecological Modeling 220:589-594.
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Author: Williams, S.E., J.L. Isaac, C.H. Graham and C. Moritz.
Title: Towards an understanding of vertebrate biodiversity in the Astralian Wet Tropics. In N. Stork and S. Turton (Eds.). Living in a dynamic tropical forest landscape.
Journal: Blackwell Publishing (in press).
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