Perfecto, I., J. H. Vandermeer, G. Lolpez Bautista, G. Ibarra Nunez, R. Greenburg, P. Bicher, and S. Langridge. 2004. Greater predation in shaded coffee farms: The role of resident neotropical Birds. Ecollogy 85:2677-2681. (perfecto_et_al._ecology.pdf, 278.0 kb, 01-13-2006)
—A test of the insurance hypothesis of biodiversity, using bird biodiversity as a driving force.
Koelle, K. and J. Vandermeer. 2004. Dispersal-induced desynchronization: from metapopulations to metacommunities. Ecology Letters 7: (koelleavandermeer.pdf, 1015.0 kb, 01-13-2006)
—Demonstrates how phase coordination between two different patches depends on the trophic level that migrates between the patches.
Jedlica, J. , J. Vandermeer, K Aviles-Vazquez, O. Barros, and I. Perfecto. 2004. Gypsy moth defoliation of oak trees and a positive response of red maple and black cherry: An example of indirect interaction. Am. Midl. Nat. 152:231-236. (jedlick_et_al.pdf, 838.0 kb, 01-13-2006)
—Evidence that black cherry and red maple in the understory respond positively to the oak defoliation caused by a gypsy moth outbreak.
Vandermeer, J. 2004. Wada basins and qualitative unpredictability in ecological models: a graphical interpretation. Ecol. Modelling 176:65-7r4. (wada_basins.pdf, 408.0 kb, 01-13-2006)
—Introduces the concept of Wada basin as a model of multiple fractal basin boundaries.
Vandermeer, J. 2004. Coupled oscillations in food webs: Balancing competition and mutualism in simple ecological models. Am. Nat. 163:857-867. (coupled_oscillations.pdf, 3576.0 kb, 01-13-2006)
—Demonstration of in-phase versus anti-phase coordination of consumer resource oscillating pairs, depending on the type of coupling between them.
Armbrecht, I., I. Perfecto, and J. Vandermeer. 2004. Enigmatic biodiversity correlations: Ant diversity responds to diverse resources. Science 304:284-286.(armbrecht_et_al.pdf, 131.0 kb, 01-13-2006)
—Twig-nesting ant biodiversity in a coffee farm in Colombia responds to the diversity of twigs offered them, even though the ant species are complete generalists.
Philpott, S. M., J. Maldonado, J. Vandermeer and I. Perfecto. 2004. Taking trophic cascades up a level: behaviorally-modified effects of phorid flies on ants and ant prey in coffee agroecosystems. Oikos 105:141-147. (philpott_et_al.pdf, 180.0 kb, 01-13-2006)
—Phorid fly parasitoids reduce foraging efficiency of ants through behavioral modification.
Vandermeer, J., I. Granzow de la Cerda, I. Perfecto, D. Boucher, J. Ruiz, and A. Kaufmann. 2004. Multiple basins of attraction in a tropical forest: Evidence for nonequilibrium community structure. Ecology 85:575-579. (multiple_basins.pdf, 267.0 kb, 01-13-2006)
—A 12-year study of post hurricane succession in a lowland tropical forest provides evidence that multiple basins exist, suggesting chance and history play important roles in tropical forest structure.
Vandermeer, J. and I. Granzow de la Cerda. 2004. Height dynamics of the thinning canopy of a tropical rain forest: 14 years of succession in a post-hurricane forest in Nicaragua. Forest Ecol. and Management 199:125-135. (vandy_granzow.pdf, 281.0 kb, 01-13-2006)
—Development of the forest canopy in its thinning phase in a post hurricane successional forest in the lowlands of Nicaragua.
Vandermeer, J. and I. Perfecto. 2005. The future of farming and conservation. Science 308:1257 (futurefarming.pdf, 351.0 kb, 01-13-2006)
—Letter to the editor criticising the model of Green et. al., (response from Green et al., also included in the pdf).
Perfecto, I., J. Vandermeer, A. Mas, L. Soto Pinto. 2005. Biodiversity, yield, and shade coffee certification. Ecol. Economics 54:435-446. (perfecto_et_al.pdf, 499.0 kb, 01-13-2006)
—An economic analysis of the relationship between yield and biodiversity conservation in the shadede coffee system.
Mascaro, J., I. Perfecto, O. Barros, D. H. Boucher, I. Granzow de la Cerda, J. Ruiz and J. Vandermeer. 2005. Aboveground biomass accumulation in a tropical wet forest in Nicaragua following a catastrophic hurricane disturbance. Biotropica 37:600-608.(File is no longer available, 01-21-2006)
—Measurements of biomass accumulation in forest plots on the Atlantic coast of Nicaragua.
Vandermeer, J. and M. Pascual. 2005. Competitive coexistence through intermediate polyphagy. Ecological Complexity, 3:37-43.. (vandermeer_pascual.pdf, 372.0 kb, 01-13-2006)
—Neither highly specialist nor highly generalist predators are effective at deterring competitive exclusion, but rather predators that exhibit an intermediate level of polyphagy can effectively provide such a mechanism.
Vandermeer, J. 2006. Omnivory and the stability of food webs. J. of Theor. Biol. 238:497-504. (omnivory_and_webs.pdf, 274.0 kb, 01-13-2006)
—Classification of the underlying structures of omnivory in a three species system with an analysis of the stability properties of various formulations of omnivory.
Vandermeer, J. 2006. Cascading thresholds to heteroclinicity in an ecosystem model. International J. of Ecodynamics 1:373-379. (vandermeercascadinghetero.pdf, 353.0 kb, 12-31-2008)
—Complex changes in stable manifolds result in chaotic attractors cascading to heteroclinicity and extinction.
Vandermeer, J. and I. Perfecto. 2006. A keystone mutualism drives pattern in a power function. Science 311:1000-1002. (keymutualism.pdf, 197.0 kb, 05-21-2006)
—Power function and its deviations in a Mexican coffee plantation are explained by an ant/scale mutualism
Vandermeer, J., H. Liere, and B. Lin. 2006. Effects of predation pressure on species packing on a resource gradient: Insights from nonlinear dynamics. Theor. Pop. Biol. 69:395-408. (File is no longer available, 05-21-2006)
—Exploration of three coupled population oscillators on a resource gradient.
Vandermeer, J. 2006. Cascading thresholds to heteroclinicity in an ecosystem model. Ecosystem Dynamics, 1:373-379. (vandyecodynamics.pdf, 353.0 kb, 08-02-2011)
—Technical note on manifold transformation to create heteroclinic cycles.
Vandermeer, J. 2007. Heteroclinic cycles in the rain forest: Insights from complex dynamics. Book chapter, please cite web reference.
(vandyheteroclinic.pdf, 528.0 kb, 03-24-2007)
—An exploration of the way in which heteroclinic cycles may be related to some of the classical issues in rain forest ecology.
Vandermeer, J., and I. Perfectol. 2007. The Agricultural Matrix and a Future Paradigm for Conservation. Cons. Bio. 21:274-277. (vandyperfconsbio.pdf, 112.0 kb, 04-14-2007)
—An editorial arguing the need to consider the agricultural matrix in conservation planning.
Vandermeer, J. 2007. Oscillating Popualtions and Biodiversity Maintenance. BioScience 56:967-975. (vandermeerbioscience.pdf, 454.0 kb, 04-14-2007)
—Argues that coupled oscillators represent a useful paradigm for examining the structure of biodiversity.
Vandermeer, J. and B. B. Lin. 2008. The importance of matrix quality in fragmented landscapes: Uniderstanding ecosystem collapse through a combination of deterministic and stochastic forces. Ecological Complexity 5:222-227.(linperfectvandybioscience.pdf, 420.0 kb, 12-31-2008)
—Nonlinear and stochastic effects create conditions for sudden ecosystem collapse in a model system.
Ferguson, B. H. Morales, A. Gonzalez Rojas, F. de Jesus Iniguez Perez, M. E. Maerrtinez Torres, Kathleen McAfee, Ron Nigh, I. Perfeto, S. M. Philpott, L. Soto Pinto, J. Vandermeer, R. M. Vidal, L. E. Avila Romero, H. Bernardino, R. Realpozo Reyes. 2009. La soberania alimentaria: Cultivando nuevas alianzas entre ampo, bosque y ciudad. Agroecología. 4:49 – 58. (ferguson_etal_2010.pdf, 3199.0 kb, 08-02-2011)
—Spanish language article about food sovereignty.
Ruiz, J., J. Vandermeer, and I. Granzow de la Cerda. 2010. Growth and mortality patterns in a thinning canopy of post-hurricane regenerating rain forest in Eastern Nicaragua (1990 – 2005). J. of Tropical Biology, 58:1283-1297. (ruizetal2010.pdf, 395.0 kb, 08-02-2011)
Late stage growth of trees in a hurricane damaged rain forest in Nicaragua.
Perfecto, I., and J. Vandermeer. 2010. The agroecological matrix as alternative to the land-sparing/agriculture intensification model. PNAS 107:5786-5791.(perfectovandypnas.pdf, 513.0 kb, 08-02-2011)
Analysis of the land sparing versus land sharing debate, emphasizing the importance of a landscape perspective.
Vandermeer, J., I. Perfecto, and N. Schellhorn. 2010. Propagating sinks, ephemeral sources and percolating mosaics: Conservation in landscapes. Landscape Ecology, 25:509-518.
(vandyperfshellhorn.pdf, 301.0 kb, 08-02-2011)
A theoretical view of landscape structure composed of different classes of patches.
Vandermeer, J. and A. King. 2010. Consequential classes of resources: Subtle global bifurcation with dramatic ecological consequences in a simple population model. J. Theoretical Biology, J. Theor. Biol. 263:237-241. (vandyking.pdf, 524.0 kb, 08-02-2011)
—Theoretical analysis of a unique kind of bifurcation resulting from distinctly different classes of resources in a Lotka Volterra framework.
Vandermeer, J. 2011. Intransitive loops in ecosystem models: from stable foci to heteroclinic cycles. Ecological Complexity, 8:92-97. (vandyintransitive.pdf, 728.0 kb, 08-02-2011)
—Some dynamic consequences of intransitive loops in Lotka Volterra competition systems.
Vandermeer, J. and S. Yitbarek. 2012. Self-organized spatial pattern determines biodiversity in spatial competition. J. of Theor. Biol. 300:48-56. (vandyyitbarekproofs.pdf, 1287.0 kb, 04-06-2013)
—Theoretical analysis of the pattern of competition coefficients and the resulting spatial pattern in a cellular automata model.
Tscharntke, Teja, Y. Clough, L. Jackson, I. Motzke, I. Perfecto, J. Vandermeer, T. C Wanger, and A Whitbread 2012. Global food security, biodiversity conservation and the future of agricultural intensification. Biological Conservation, doi:10.1016/j.biocon.2012.01.068. (tscharntkeetal.pdf, 362.0 kb, 04-06-2013)
—Opinion piece concerning the debate between land sparing and land sharing.
Scheffer, M., S. Carpenter, T. M. Lenton, J. Bascompte, W. Brock, V. Dakos, J. van den Koppel, I. van de Leemput, S. Levin, E. H. van Nes, M. Pascual, J. Vandermeer. 2012. Anticipating critical transitions. Science, 338:344 – 348. (shefferetal.pdf, 793.0 kb, 04-06-2013)
—Summary of recent advances in anticipating critical transitions.
Vandermeer, J. 2012. Forcing by rare species and intransitive loops creates distinct bouts of extinction events conditioned by spatial pattern in competition communities. Theoretical Ecology, DOI 10.1007/s12080-012-0175-z. (vandyrarespptheorecol.pdf, 1743.0 kb, 04-06-2013)
—Detailed analysis of one particular competition matrix in the model of Vandermeer and Yitbarek, especially regarding the intransitive loops in the system.
Page, S., and J. Vandermeer. 2013. Inequality and Innovativeness. Social Sciences Research Network. http://ssrn.com/abstract=2227002 (pagevandermeer.pdf, 384.0 kb, 04-06-2013)
—Model and data relating country level innovativeness and economic inequality.