Evolution,   Systems   Biology,   &   Statistical   Phylogenomics

  • Haeckel's Trunk
  • Eubacteria
  • Bacteriophages

Jonathan P. Bollback

Short Bio:

I was born in north-western Pennsylvania in 1971. In the autumn of 1990, after free-lancing as a photographer, I enrolled in the B.Sc Environmental Sciences program at the State University of New York (College at Purchase) with a focus in Environmental Organic Chemistry. At the start of my third year I took a course in vertebrate evolution. During the course I realized that I wanted to study evolutionary biology. In the autumn of 1993 I transferred to the University of Maryland to pursue my studies in evolutionary biology. I earned my B.Sc degree in 1995.

After completing my undergraduate studies I continued with graduate studies at Maryland in the Department of Zoology and at the Smithsonian’s National Museum of Natural History Laboratory of Molecular Systematics. Between 1995-1998 I was a Pre-doctoral Fellow at the Smithsonian.

In the fall of 1998, I began my Ph.D. work on experimental evolution and statistical phylogenetics with John Huelsenbeck at the University of Rochester, New York. I earned my Master of Science degree in 2000 in Evolutionary Genetics and then my Ph.D. in October of 2004.

After completing my Ph.D. I moved to the University of Copenhagen, Denmark to work with Rasmus Nielsen on a number of problems in statistical genetics. I worked in Denmark from the autumn of 2004 until the spring of 2008. I then moved from Copenhagen to the University of Edinburgh, Scotland to work with Andrew Leigh-Brown and Andrew Rambaut on the evolutionary dynamics of influenza.

Research Interests:

My research focuses on understanding evolutionary constraints. To better understand constraints my group focuses on four focal areas: horizontal gene transfer (HGT), gene regulation, costs and benefits of immunity, and the properties of mutations.


Senior Lecturer
2016 to Current
Functional and Comparative Genomics
Institute of Integrative Biology
University of Liverpool
Biosciences Building
Liverpool, L69 7ZB, UK

Assistant Professor
2010 to 2016
Institute of Science and Technology Austria (IST Austria)
Am Campus 1
A – 3400 Klosterneuburg, Austria

Post-doctoral Researcher
2008 to 2010
School of Biological Sciences
Institute of Evolutionary Biology
University of Edinburgh
Advisor: Andrew Rambaut and Andy Leigh Brown

Post-doctoral Researcher
2004 to 2008
Department of Biology, Evolutionary Biology
University of Copenhagen, Denmark
Advisor: Rasmus Nielsen

Ph.D. Evolutionary Genetics
October, 2004
University of Rochester, USA
Advisor: John Huelsenbeck
Thesis title: Experimental bacteriophage evolution and theoretical systematics

M.Sc. Evolutionary Genetics
December, 2000
University of Rochester, USA
Advisor: John Huelsenbeck

B.Sc. Biology
August, 1995
University of Maryland at College Park, USA


Mato Lagator, Claudia Igler, Anaisa Moreno, Calin Guet, J. P. Bollback. (2016) Epistatic interactions in the Arabinose cis regulatory element. Molecular Biology and Evolution 33(3): 761-769.

Anne Kupczok and J. P. Bollback. (2014) Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics 15:663.

Melissa J. Ward, Samantha J. Lycett, Dorita Avila Rojas, J. P. Bollback and Andrew J. Leigh Brown. (2013) Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology 13:222.

Rodrigo Redondo, Anne Kupczok, Gertraude Stift, and J. P. Bollback. (2013) Complete genome sequence of the novel phage MG-B1 infecting Bacillus weihenstephanensis. Genome Announcements 1 (3), e00216-13.

Anne Kupczok and J. P. Bollback. (2013) Probabilistic models for CRISPR spacer content evolution. BMC Evolutionary Biology 13:54.

Peter Gravlund, Kim Aaris-Sorensen, Michael Hofreiter, Matthias Meyer, J. P. Bollback, Nanna Noe-Nygaard. (2012) Ancient DNA extracted from Danish aurochs (Bos primigenius): Genetic diversity and preservation. Annals of Anatomy 194:103-111.

Caitriona M. Guinane, Nouri L. Ben Zakour, Maria A. Tormo-Mas, Lucy A. Weinert, Bethan V. Lowder, Robyn A. Cartwright, Davida S. Smyth, Cyril J. Smyth, Jodi Lindsay, Katherine A. Gould, Adam Witney, Jason Hinds, J. P. Bollback, Andrew Rambaut, José Penadés, and J. Ross Fitzgerald. (2010) Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biology and Evolution 2:454-466.

Bollback, J. P. and John P. Huelsenbeck. (2009) Parallel genetic evolution within and among bacteriophage species of varying degrees of divergence. Genetics 181: 225–234.

Bollback, J. P., T. L. York, R. Nielsen. (2008) Estimation of 2Nes from temporal allele frequency data. Genetics 179: 497–502.

Petersen, L., J. P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen. (2007) Genes under positive selection in Escherichia coli. Genome Research 17:1336-1343.

Bollback, J. P. and John P. Huelsenbeck. (2007) Clonal interference is alleviated by high mutation rates in large populations. Mol. Biol. and Evol. 24(6):1397–1406.

Binladen, J., M. T. P. Gilbert, J. P. Bollback, F. Panitz, C. Bendixen, R. Nielsen, E. Willerslev. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE. 2(2): e197.

Freyhult, E., J. P. Bollback, and Paul P. Gardner. (2007) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on non-coding RNA. Genome Research 17(1):117-125.

Bollback, J. P., P. P. Gardner, and R. Nielsen. (2007) Estimating the history of mutations on a phylogeny. In "Ancestral Sequence Reconstruction" (Liberles, D. Ed.) Oxford University Press, UK. 31 May 2007.

Reynolds, S. M., K. Dryer, J. P. Bollback, J. A. C. Uy, G. L. Patricelli, T. Robson, G. Borgia, and M. J. Braun (2007) Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk. 124(3):857-867.

Bollback, J. P. (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7:88.

Conn, J. E., J. H. Vineis, J. P. Bollback, D. Y. Onyabe, R. C. Wilkerson and M. M. Povoa. (2006) Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil. Am. J. Trop. Med. Hyg. 74(5): 798-806.

Betancourt, A. J. and J. P. Bollback. (2006) The mutational landscape model in experimental evolution. Current Opinions in Genetics and Development. 16:618-623.

Bollback, J. P. (2005) Posterior mapping and predictive distributions. In "Statistical methods in Molecular Evolution" (Nielsen, R. Ed.) Springer Verlag New York, Inc. New York, USA.

Harshman, J., C. J. Huddleston, J. P. Bollback, T. J. Parsons, and M. J. Braun. (2003) True and false gavials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 52(3): 386-402.

Huelsenbeck, J. P., R. Nielsen, J. P. Bollback. (2003) Stochastic mapping of morphological characters. Sys. Biol. 52(2):131-158.

Bollback, J. P. (2002) Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19 (7): 1171-1180.

Huelsenbeck, J. P., J. P. Bollback, and A. Levine. (2002) Inferring the root of a phylogenetic tree. Sys. Biol. 51 (1): 32-43.

Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294: 2310-2314.

Conn, J. E., J. P. Bollback, D. Y. Onyabe, T. N. Robinson, R. C. Wilkerson, and M. M. Povoa. (2001) Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi. Mol. Ecol. Notes. 1 (4): 223-225.

Huelsenbeck, J. P., and J. P. Bollback. (2001) Empirical and hierarchical Bayesian estimation of ancestral states. Sys. Biol. 50 (3): 351-366.

Huelsenbeck, J. P. and J. P. Bollback. (2001) Application of the likelihood function in phylogenetic analysis. In "Handbook of Statistical Genetics" (Balding. D.J., Bishop, M., and Cannings, C., Eds.) Chapter 15, pp. 415-439. John Wiley and Sons, Inc. New York, USA.

Bollback, J. P., and John P. Huelsenbeck. (2001) Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). J. Mol. Evol. 52: 117-128.


Curriculum vitae:

My CV can be downloaded here () as a PDF.

Contact Details:

Functional and Comparative Genomics
Institue of Integrative Biology
University of Liverpool
Biosciences Building
Liverpool, L69 7ZB, UK



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