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New England Complex Systems Institute
238 Main Street Suite 319, Cambridge, MA 02142
Phone: 617-547-4100 Fax: 617-661-7711

NECSI’s research into evolution clarifies basic issues in evolutionary dynamics such as how altruism arises, the origin and characterization of biodiversity, as well as the interplay of evolution with ecology. Specific work addresses:

  • Patterns in Space and the Dynamics of Evolution
  • The gene-centered view as a dynamic version of the mean field approximation
  • Biodiversity and spatial symmetry breaking
  • Genealogical trees and biodiversity
  • Estimating the diversity of a population from a sample
  • Evidence for why reproductive fitness isn’t necessarily predictive of long term survival
  • Environment modification and inheritance
  • Origins of altruism, including altruism by social signaling
  • Sewall Wright's shifting balance theory
  • Cellular automata models of evolutionary self-replication

Publications, Books & Edited Volumes

E. M. Baptestini, M. A. M. de Aguiar, Yaneer Bar-Yam, Conditions for neutral speciation via isolation by distance. Journal of Theoretical Biology (in press, 2013).

A. B. Martins, M. A. M. de Aguiar, and Yaneer Bar-Yam, Evolution and Stability of Ring Species. PNAS 201217034 (March 11, 2013). Available here.

David M. Schneider, Eduardo de Carmo, Yaneer Bar-Yam, Marcus A.M. de Aguiar, Robustness against extinction by stochastic sex determination in small populations, Phys. Rev. E 86, 041104 (2012), (October 2, 2012). Full Paper on arXiv

Elizabeth M. Baptestini, Marcus A.M. de Aguiar, Yaneer Bar-Yam, The role of sex separation in neutral speciation.Theoretical Ecology, pg 1-11 (2012). Full Paper on arXiv. Overview on Speciation

Blake C. Stacey, Andreas Gros, Yaneer Bar-Yam, Beyond the Mean Field in Host-Pathogen Spatial Ecology. arXiv:1110.3845, October 5, 2011. PDF File

Marcus A.M. de Aguiar, Yaneer Bar-Yam, The Moran model as a dynamical process on networks and its implications for neutral speciation, Phys. Rev. E 84, 031901 (2011), DOI:10.1103/PhysRevE.84.031901. Full Paper on arXiv Overview on Speciation

Y.E. Maruvka, N.M. Shnerb, Y. Bar-Yam, J. Wakeley, Recovering Population Parameters from a Single Gene Genealogy: An Unbiased Estimator of the Growth Rate, Molecular Biology and Evolution 2010, doi: 10.1093/molbev/msq331. Abstract PDF file

M.J. Wade, D.S. Wilson, C. Goodnight, D. Taylor, Y. Bar-Yam, M.A.M. de Aguiar, B. Stacey, J. Werfel, G.A. Hoelzer, E.D. Brodie III, P. Fields, F. Breden, T.A. Linksvayer, J.A. Fletcher, P.J. Richerson, J.D. Bever, J.D. Van Dyken, P. Zee, Multilevel and kin selection in a connected world. Nature 463, E8-E9 (2010). PDF File

M.A.M. de Aguiar, M. Baranger, E.M. Baptestini, L. Kaufman, Y. Bar-Yam, Global Patterns of Speciation and Diversity, Nature 460, 384-387 (2009). abstract and full paper press release

B. Allen, M. Kon, Y. Bar-Yam, A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats, The American Naturalist 174 (2009). PDF file press release

Pierre D. M., D. Goldman, Y. Bar-Yam & A. S. Perelson: Somatic evolution in the immune system: the need for germinal centers for efficient affinity maturation. J. Theor. Biol. 186, 159-171 (1997) PDF file

C. Goodnight, E. Rauch, H. Sayama, M. de Aguiar, M. Baranger, and Y. Bar-Yam, Evolution in Spatial Predator-Prey Models and the "Prudent Predator": The Inadequacy of Steady-State Organism Fitness and the Concept of Individual and Group Selection. Complexity 13, pg. 23-44 (2008). PDF file.

H. Sayama, L. Kaufman, and Y. Bar-Yam, Spontaneous pattern formation and diversity in spatially structured evolutionary ecology, in Focus on Biodiversity Research, Jan Schwartz, Ed. (Nova Science Publishers, in press). PDF file

E. M. Rauch, Y. Bar-Yam, Long-range interactions and evolutionary stability in a predator-prey system, Physical Review E 73, 020903 (2006). abstract PDF file press release

E. M. Rauch, Y. Bar-Yam, Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat areas, PNAS 102, 9826-9829 (July 12, 2005). abstract PDF file (requires subscription)

E. M. Rauch, Y. Bar-Yam, Theory predicts uneven distribution of genetic diveristy within species, Nature 431, 449-452 (Sept. 23, 2004). PDF file

J. K. Werfel, Y. Bar-Yam, The evolution of reproductive restraint through social communication,PNAS 101, pp. 11019-11024, 2004. PDF file press release videos

M. A. M. de Aguiar, E. M. Rauch, Y. Bar-Yam, Invasion and extinction in the mean field approximation for a spatial host-pathogen model, Journal of Statistical Physics 114, 1417-1451 (2004). PDF file

M. A. M. de Aguiar, M. Baranger, Y. Bar-Yam, H. Sayama, Robustness of spontaneous pattern formation in spatially distributed genetic populations, Brazilian Journal of Physics 33, 514 (2003).

H. Sayama, L. Kaufman, M. A. M. de Aguiar, E. Rauch, C. Goodnight, Y. Bar-Yam, Breakdown of the gene-centered view: What is beyond Neo-Darwinian evolution? Proceedings of the Fourth International Conference on Complex Systems. Perseus Books/InterJournal (2002).

E. M. Rauch, M. A. M. de Aguiar, Y. Bar-Yam, Mean field approximation to a spatial host-pathogen model, Phys. Rev. E 67, 047102 (2003). PDF file

Y. Bar-Yam, Complex Systems and Sports, 2003. PDF file

H. Sayama, M. A. M. de Aguiar, Y. Bar-Yam, M. Baranger, Interplay between Turing pattern formation and domain coarsening in spatially extended population models, FORMA 18 (2003). (Also available at PDF file)

H. Sayama, L. Kaufman, Y. Bar-Yam, Spontaneous pattern formation and genetic diversity in habitats with irregular geographical features, Conservation Biology 17, 893 (2003).

E. M. Rauch, H. Sayama, Y. Bar-Yam, Dynamics and genealogy of strains in spatially extended host pathogen models, J Theor Biol 221, 655-664 (2003). PDF file

M. A.M. de Aguiar, H. Sayama, E. Rauch, Y. Bar-Yam, M. Baranger, Stability and instability of polymorphic populations and the role of multiple breeding seasons in phase III of Wright's shifting balance theory, Phys Rev E 65, 031909 (2002). PDF file

E. Rauch, H. Sayama, Y. Bar-Yam, Relationship between measures of fitness and time scale in evolution, Phys Rev Lett 88, 228101 (2002).PDF file

H. Sayama, M.A.M. de Aguiar, Y. Bar-Yam, M. Baranger, Spontaneous pattern formation and genetic invasion in locally mating and competing populations, Phys Rev E 65, 051919 (2002). PDF file

H. Sayama, Y. Bar-Yam: The gene centered view of evolution and symmetry breaking and pattern formation in spatially distributed evolutionary processes, Nonlinear Dynamics in the Life and Social Sciences, W. Sulis and I. Trofimova, Eds. (NATO Science Series A/320, IOS Press, 2001) 360-368. PDF file

H. Sayama, Self-Replicating Worms That Increase Structural Complexity Through Gene Transmission, in Artificial Life, M. A. Bedau, J. S. McCaskill, N. H. Packard, S. Rasmussen, Eds. (MIT Press, 2000) 21-30. PDF file PostScript (gzipped)

H. Sayama, L. Kaufman, Y. Bar-Yam, Symmetry breaking and coarsening in spatially distributed evolutionary processes including sexual reproduction and disruptive selection, Physical Review E 62, 7065-7069 (2000). PDF file

Y. Bar-Yam, Formalizing the gene-centered view of evolution, in Advances in Complex Systems 2, 277-281 (1999). PDF file article

H. Sayama, A new structurally dissolvable self-reproducing loop evolving in a simple cellular automata space, Artificial Life 5, 4, 343-365 (1999). Full text (PDF file)

H. Sayama, L. Kaufman, Y. Bar-Yam, The role of spontaneous pattern formation in the creation and maintenance of biological diversity, , Brief Article 417, accepted.

Y. Bar-Yam, H. Sayama, Formalizing the gene-centered view of evolution, InterJournal, Brief Article 385, accepted.

H. Sayama, Spontaneous evolution of self-reproducing loops on cellular automata, InterJournal, Brief Article 236, accepted.

Y. Bar-Yam, Making Things Work, Chapter 6 and 7.

Photo © James Seith