Publications

Authors in Bold are members of the Ponciano lab!

Work in Progress (tentative titles):

  1. With C. Baer. Joint likelihood inference of the distribution of fitness effects from recombinant inbreds derived from mutation accumulation lines
  2. With L.J. Forney and Jacques Ravel at UI: Understanding the community dynamics of the vaginal microbial flora.
  3. With Bill Pine. In depth investigation of the Binomial-Poisson sampling model for abundance estimation in wildlife studies.
  4. With Ari Martinez, Scott Robinson, John Terborgh. Tropical Avian Diversity, Behavior and Ecological Change in the Peruvian Amazon: what have we learned in thirty years?
  5. With Ari Martinez.  Do Birds Cry Wolf? – Assumptions and Challenges of Identifying Avian Deceptive Behavior in the Peruvian Amazon.
  6. Leveraging existing international collaborations to pivot epidemiological modeling to address timely SARS-CoV19 forecasting in Latin America. Jason K. Blackburn, Juan Ponciano, Juan Pablo Gomez, Robert Holt, Jose M. Ponciano

Papers “In review”:

  1. Hannah Holland-Moritz , Julia E. M. Stuart , Lily R. Lewis , Samantha N. Miller , Michelle C. Mack , Jose Miguel Ponciano , Stuart F. McDaniel , Noah Fierer. In review.The bacterial communities of Alaskan mosses and their contributions to N2-fixation.
  2. Julia E. M. Stuart, Hannah Holland-Moritz, Lily R. Lewis, Mélanie Jean, Samantha N. Miller, Stuart F. McDaniel, Noah Fierer, José Miguel Ponciano, and Michelle C. Mack. In review. Host taxonomic identity as a driver of moss-associated N2 fixation rates in Alaska
  3. Ponciano, J.M., Ponciano, J.A., Gomez, J.P., Holt, R.D. and Jason K Blackburn. In review. Poverty levels, societal and individual heterogeneities explain the SARS-CoV-2 pandemic growth in Latin America
  4. ML Taper, SR Lele, JM Ponciano, B Dennis. In Prep. Assessing the uncertainty in statistical evidence with the possibility of model misspecification using a non-parametric bootstrap. arXiv preprint arXiv:1911.06421
  5.  Morgan A. Walker, Maria Uribasterra, Valpa Asher, José Miguel Ponciano, Sadie J. Ryan and Jason K. Blackburn. In Review. Ungulate use of locally infectious zones in a re-emerging anthrax risk area. Royal Society Open Science.
  6.  Michael H. Norris, Alexander Kirpich, Andrew P. Bluhm, Diansy Zincke, Ted Hadfield, Jose Miguel Ponciano, Jason K. Blackburn. In Review. Alteration of exosporium surface oligosaccharides: Evidence of convergent patho-evolution in Bacillus anthracis. PLOS Biology

Printed Publications:

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2020

  1. Jordt, H., Stalder, T., Kosterlitz, O., Ponciano, J.M., Top, E.M. and Kerr, B., 2020. Coevolution of host–plasmid pairs facilitates the emergence of novel multidrug resistance. Nature Ecology & Evolution, pp.1-7.
  2. Easterday, R., Ponciano, J.M., Gómez, J.P.,Van Ert, M.N., Hadfield, T., Bagamian, K., Blackburn, J.K., Stenseth, N.C. and W.C. Turner. 2020. Coalescence modeling of intrainfectoin Bacillus anthracis populations allows estimation of infection parameters in wild populations. Proceedings of the National Academy of Sciences.Available from PNAS Early Contents webpage: https://doi.org/10.1073/pnas.1920790117

2019

  1. Gomez, J.P., Ponciano, J.M., Londoño, G. and Robinson, S.K. 2019. The biotic interactions hypothesis partially explains bird species turnover along a lowland Neotropical precipitation gradient. Global Ecology and Biogeography vol 00:1-12. DOI: 10.1111/geb.13047
  2. Ponciano, J.M. and M.L. Taper. 2019. Model Projections in Model Space: A geometric interpretation of the AIC allows estimating the distance between truth and approximating models. Frontiers in Ecology and Evolution. Vol 7, article 413, doi: 10.3389/fevo.2019.00413
  3. Dennis, B., Ponciano, J.M., Taper, M.L. and S.R. Lele. 2019. Errors in statistical inference under model misspecification: evidence, hypothesis testing, and AIC. Frontiers in Ecology and Evolution.  Vol 7, article 372, doi: 10.3389/fevo.2019.00972
  4. Picardi, S., Basille, M. Peters, W., Ponciano, J.M., Boitani, L. and F. Cagnacci. 2019. Movement responses of Roe Deer to hunting risk. The Journal of Wildlife Management. 83(1):43-51.
  5. Blohm, G., Gulbudak, H., Martcheva, M. and J.M. Ponciano. 2019 Modeling intracellular replication of flaviviruses. In: “Mosquitos: Species Distribution and Disease“. Editor: Tabitha Terry. Nova Science Publishers.
  6. Blackburn, J.K., Ganz, H.H., Ponciano, J.M., Turner, W.C., Ryan, S.J., Kamath, P., Cizauskas, C., Kausrud, K., Holt, R.D., Stenseth, N.C. and Getz, W.M., 2019. Modeling R0 for Pathogens with Environmental Transmission: Animal Movements, Pathogen Populations, and Local Infectious Zones. International journal of environmental research and public health, 16(6), p.954.

2018

  1. Ponciano, J.M., Taper, M.L. and B. Dennis. 2018. The loss of history and the strength of density dependence. Theoretical Population Biology. 121:45-59
  2. Gomez, J.P.*, Nekorchuk, D.M., Mao, L., Ryan, S.J∗∗., Ponciano J.M. and Blackburn, J.K**. 2018. Decoupling environmental effects and host population dynamics for anthrax, a classic reservoir-driven disease.PLOS ONE. 13(12):e0208621.
  3. 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. 2018 6(3): e1037
  4. Ponciano, J.M. 2018. A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: linking ecological, population genetics and evolutionary processes. Theoretical Population Biology. 122:128-136.
  5. 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. 143:177-191.

2017

  1. 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
  2. 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
  3. 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.

2016

  1. 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.
  2. 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: 10.3732/ajb.1500408.
  3. 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
  4. 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.
  5. 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.
  6. 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
  7. 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.

2015

  1. Ferguson, J., Carvalho, F., Murillo, O. and J.M. Ponciano. 2015. Population growth, density dependence and evironmental autocorrelation in animal populations.  Theoretical Ecology, 8(2):doi 10.1007/s12080-015-0276-6
  2. 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.
  3. 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.

2014

  1. 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.
  2. 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.
  3. 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.

2013-2010 (First 3 years at UF)

  1. 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.
  2. 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
  3. 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.
  4. 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.
  5. Ponciano J.M. and M. Capistrán. 2011. First principles modeling of nonlinear incidence rates in seasonal epidemics. PLoS Computational Biology, 7(2):e1001079.
  6. Dennis, B., Ponciano J.M. and M.L. Taper. 2010. Replicated sampling increases efficiency in monitoring biological populations. Ecology 91(2): 610-620.

2009-2007 (Center for Research in Mathematics CIMAT, Guanajuato, México)

    1. 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.
      1. 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.
  1. 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.
  2. 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
  3. 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.

2006-2004 (at Univ. of Idaho, as a PhD student)

  1. 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.
  2. 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.
  3. 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.
  4. 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.