Authors in Bold are members of the Ponciano lab!

Work in Progress (tentative titles):

  1. Ponciano, J.M. and L. Harmon. First principles derivation of alternative models of phenotypic evolution. Prepared for Evolution
  2. Ponciano, J.M., Andersen, E. and C. Baer. Joint likelihood inference of the distribution of fitness effects from recombinant inbreds derived from mutation accumulation lines
  3. Ponciano, J.M., Gomez, J.P., Forney, L.J. Understanding the community dynamics of the vaginal microbial flora
  4. Gomez, J.P., Ponciano, J.M. and S. Robinson. Asymmetric effects of environmental filtering on the assembly of tropical bird communities along a moisture gradient. Prepared for Journal of Animal Ecology.
  5. McDaniel, S., Payton, A., Norrell, T., Jones, K. and J.M. Ponciano.  Suppressed recombination, epistasis and genetic variation for meiotic sex ratio in Ceratodon purpureus.

In review:

  1. Ponciano, J.M.*, Taper, M.L. and B. Dennis. The loss of history and the strength of density dependence. Prepared for the Journal of Biological Dynamics. * Corresponding author. Theoretical Population Biology. In review since February 2017 (Sigh…)
  2. Zenil-Ferguson, R., Burleigh, J.G. and J.M. Ponciano. Chromploid- an R package for chormosome number evolution across the plant tree of life. Applications in Life Sciences. October 2017

Printed Publications:

*Copyright Notice* This material is presented to ensure timely dissemination of scholarly and technical work.  Copyright and all rights therein are retained by authors or by other copyright holders.  All persons copying this information are expected to adhere to the terms and constraints invoked by each author’s copyright. In most cases, these works may not be re-posted without the explicit permission of the copyright holder.

  1. Ponciano, J.M. A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: linking ecological, population genetics and evolutionary processes. Theoretical Population Biology. Accepted Oct. 27th 2017.
  2. H.J. Brockmann, St. Mary, C.M. and José Miguel Ponciano. 2017. Discovering structural complexity and its causes: breeding aggregations in Horseshoe Crabs. Animal Behaviour. Accepted Sept 22nd 2017.
  3. Loftie-Eaton W, Bashford K, Quinn H, Dong K, Millstein J, Hunter S, Thomason M, Merrikh H, Ponciano J.M. and Eva M. Top. (Ponciano and Top corresponding authors). 2017 . Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nature Ecology & Evolution. DOI: s41559-017-0243-2
  4. Gomez, J.P. †, Robinson, S.K.**, Blackburn, J.K.** and José M. Ponciano (corresponding author). 2017. An efficient extension of N-mixture models for multi-species abundance estimation. Methods in Ecology and Evolution, DOI:10.1111/2041-210X.12856
  5. Zenil-Ferguson, R. †, José M. Ponciano and J. Gordon Burleigh**. 2017. Testing the association of phenotypes with polyploidy: an example using herbaceous and woody eudicots. Evolution. DOI:10.1111/evo.13226 . Rosana Zenil-Ferguson won the Ernst Mayr Award at the Evolution meetings 2017 with this paper.
  6. Gil, M., Zill, J. and J.M. Ponciano. 2016.Context-dependent landscape of fear: algal density elicits risky herbivory in a coral reef. Accepted in Ecology, DOI 10.1002/ecy.1668.
  7. Zenil-Ferguson, R., Ponciano, J.M. and J.G. Burleigh. 2016. The role of genome downsizing and genome size thresholds on the distribution of Angiosperms genome sizes. American Journal of Botany, DOI: .
  8. Farhadifar, R., Ponciano, J.M., Andersen, E.C., Needleman, D.J., and C.F. Baer.  2016. Mutation is a sufficient and robust predictor of genetic variation for mitotic spindle traits in C. elegans. Genetics: Early Online, published on June 22, 2016 as 10.1534/genetics.115.185736
  9. Loftie-Eaton, W., Burleigh, S., Simmons, R., Hunter, S., Settles, M., Ponciano, J. M*. and E. M. Top*. 2016. Evolutionary paths that expand plasmid host-range and increase persistence: implications for the spread of antibiotic resistance. Molecular Biology and Evolution. * Corresponding authors.
  10. Martinez, A., Gomez-Echeverri, J.P.,  Ponciano, J.M. and Robinson, S. 2016. Functional traits, Flocking Propensity, and Perceived Predation Risk in an Amazonian Understory Bird Community. The American Naturalist 187 (5).DOI: 10.1086/685894.
  11. Taper, M.L. and J.M. Ponciano. 2016. Evidential Statistics as a statistical modern synthesis to support 21st century science. Population Ecology. DOI: 10.1007/s10144-015-0533-y
  12. Taper, M.L. and J.M. Ponciano. 2016. Projections in Model Space: Multi-model inference beyond model averaging. Appendix to: Bandyopadhyay, P., Gordan Brittan , and Mark L. Taper. 2015. Belief, Evidence, and Uncertainty:Problems of Epistemic Inference. Springer Monographs in Philosophy of Science. Appeared March 2016.
  13. Ferguson, J., Carvalho, F., Murillo, O. and J.M. Ponciano. 2015. Population growth, density dependence and evironmental autocorrelation in animal populationsTheoretical Ecology, 8(2):doi 10.1007/s12080-015-0276-6
  14. Ferguson, J.M. and J.M. Ponciano. 2015. Evidence and implications of higher order scaling in the environmental variation of animal population growth. Proceedings of the National Academy of Sciences. 112(9): doi: 10.1073/pnas.1416538112.
  15. Etienne, V., Andersen, E., Ponciano, J.M., Blanton D., Cadavid, Joyner-Matos, J., Chikako, M., Tabman, B. and C. Baer. 2015. The red death meets the abdominal bristle: Polygenic mutation for susceptibility to a bacteria pathogen in Caenorhabditis elegans. Evolution, 69(2): 508-519.
  16. Dennis, B. and J.M. Ponciano. 2014. Density dependent state space model for population abundance data with unequal time intervals.  Ecology 95(8):2069-2076.
  17. Carvalho, F., Ahrens, R., Murie, D., Ponciano, J.M., Aires-da-Silva, A., M. Maunder and F. Hazin. 2014. Incorporating specific change points in catchability in fisheries stoch assessment models: An alternative approach applied to the blue shark (Prionace glauca) stock in the south Atlantic Ocean. Fisheries Research, 154:135-146.
  18. Ferguson, J.M. and J.M. Ponciano. 2014. Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series. Ecology Letters 17: 251-259.
  19. Barbour, A.B., Ponciano, J.M. and Kai Lorenzen. 2013. Apparent survival estimation from continuous mark-recapture/resighting data.  Methods in Ecology and evolution, 4(9):846-853. doi: 10.1111/2041-210X.12059.
  20. Tyreman, J.G., Ponciano J.M., Joyce, P., Forney, L.J. and L.J. Harmon. 2013 The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms. BMC Evolutionary Biology, 13:22,  doi:10.1186/1471-2148-13-22
  21. Vander Zanden, H., Bjorndal, K.A., Musting, W., Ponciano, J.M., Bolten, A.B. 2012. Inherent variation in stable isotope values and disrcrimination factors in two life stages of green turtles. Physiological and Biochemical Zoology, 85(5):431-441.
  22. Ponciano, J.M., Burleigh, G., Braun, E. and M.L. Taper. 2012. Assessing parameter identifiability in Phylogenetic models using Data Cloning. Systematic Biology, 61(6):955-972.
  23. Ponciano J.M. and M. Capistrán. 2011. First principles modeling of nonlinear incidence rates in seasonal epidemics. PLoS Computational Biology, 7(2):e1001079.
  24. Dennis, B., Ponciano J.M. and M.L. Taper. 2010. Replicated sampling increases effi- ciency in monitoring biological populations. Ecology 91(2): 610-620.
  25. Ponciano J.M., La J.H, Joyce P. and L.J. Forney. 2009. Evolution of Diversity in Spatially Structured E. coli populations. Appl. Env. Microbiol. 75(19): 6047-6054.
  26. Ponciano, J.M., Mark L. Taper, Brian C. Dennis and Subhash R. Lele. 2009. Hierarchical models in Ecology: Confidence intervals, hypothesis testing and model selection using data cloning. Ecology 90(2):356-362.
  27. De Gelder L., Williams J.J., Ponciano J.M., Sota M. and E.M. Top. 2008. Adaptive plasmid evolution results in host range expansion of a broad-host-range plasmid. Genetics 178: 2179-2190.
  28. Ponciano J.M., De Gelder L, Top E.M. and P. Joyce. 2007. The population biology of bacterial plasmids: a Hidden-Markov Model approach. Genetics, 176(2):957-968 .Supplemental file
  29. De Gelder L., Ponciano J.M., Joyce P., and E.M. Top. 2007. Stability of the broad host range Inc-P-1beta plasmid pB10: no guarantees for a long term association.Microbiology, 153: 452-463.
  30. Dennis B., Ponciano J.M., Lele S., Taper M. and D. Staples. 2006. Estimating density dependence, process noise and observation error. Ecological Monographs 76(3):323-341.
  31. Ponciano J.M., Vandecasteele F, Hess T., Forney L.J., Crawford R.L. and P. Joyce. 2005. A stochastic approach to model the effect of environmental factors on bacterial growth. Appl Envrion Microbiol. 71:2355-2364.
  32. Joyce P., Abdo Z., Ponciano J.M., L. De Gelder, L.J. Forney and E.M. Top. 2005. Modeling the impact of periodic bottlenecks, unidirectional mutation and observational error in experimental evolution. J. of Math. Biol. 50: 645-662.
  33. De Gelder L., Ponciano J.M.,Abdo Z, Joyce P, Forney L.J. and E.M. Top. 2004. Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic sensitive mutants in a population of resistant bacteria during experimental evolution. Genetics 168:1131-1144.

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