Joshua B. Plotkin

Professor of Biology, Mathematics (secondary), and Computer & Information Science (secondary)
219 Carolyn Lynch Laboratory
Research Interests: 

I use mathematics and computation to study questions in evolutionary biology and ecology.  Research in the group is concerned primarily with adaptation in populations. Related interests include the evolution of robustness and adaptability, the evolutionary ecology of viral populations, the nature of genetic drift, the dynamics of protein translation, and the evolution of social norms (read more).


Junior Fellow, Harvard Society of Fellows, 2007
PhD, Princeton University, 2003
AB, Harvard College, 1999

Board of Reviewing Editors, Science (AAAS)
Editorial Board, Cell Reports

Selected Publications (Google Scholar):

Newberry MG, Ahern C, Clark R, Plotkin JB. Detecting evolutionary forces in language change. Nature 551: 223-226 (2017) [pdf]

Plotkin JB. No escape from the tangled bank. Nature 551: 42-43 (2017) [pdf]

Stewart A, Parsons T, Plotkin JB. Evolutionary consequences of behavioral diversity. PNAS 113: 7003-7009 (2016) [pdf]

Nourmohammad A, Otwinowski J, Plotkin JB. Host-pathogen co-evolution and the emergence of broadly neutralizing antibodies in chronic infections. PLOS Genetics 12: 1006171 (2016) [pdf]

Shah P, McCandlish M, Plotkin JB. Contingency and entrenchment in protein evolution under purifying selection. PNAS 112:3226–3235 (2015) [pdf]

Stewart A, Plotkin JB. Collapse of cooperation in evolving games. PNAS 111: 17558-17563 (2014) [pdf]

Otwinowski J, Plotkin JB. Inferring fitness landscapes by regression produces biased estimates of epistasis. PNAS 111:2301-2309 (2014) [pdf]

Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell 153:1589-1601 (2013) [pdf]

Stewart A, Plotkin JB. From extortion to generosity, evolution in the Iterated Prisoner's Dilemma. PNAS 110: 15348-15353 (2013) [pdf]

McCandlish D, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature 497: E1-E2 (2013) [pdf]

Morlon H, Parsons T, Plotkin JB. Reconciling molecular phylogenies with the fossil record. PNAS 108: 16327–16332 (2012) [pdf][cover]

Lipsitch M, Plotkin JB, Simonsen L, Bloom B. Evolution, safety, and highly pathogenic influenza viruses. Science 336:1529-153 (2012)  [pdf]

Der R, Epstein C, Plotkin JB. Generalized population models and the nature of genetic drift. Theoretical Population Biology 80: 80–98 (2011) [pdf]

Kryazhimskiy S, Draghi J, Plotkin JB. In evolution, the sum is less than its parts. Science 332: 1160-1161 (2011) [pdf]

Kryazhimskiy S, Dushoff J, Bazykin G, Plotkin JB. Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genetics 7: 1001301 (2011) [pdf]

Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nature Reviews Genetics 12:32-42 (2011) [pdf]

Draghi J, Parsons T, Wagner G, Plotkin JB. Mutational robustness can facilitate adaptation. Nature 426: 353–355 (2010) [pdf]

Morlon H, Potts M, Plotkin JB. Inferring the dynamics of diversification: a coalescent approach. PloS Biology 8: 1000493 (2010) [pdf]

Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258 (2009) [pdf]

Kryazhimskiy S, Tkacik G, Plotkin JB. The dynamics of adaptation on correlated fitness landscapes. PNAS 106: 18638-18643 (2009) [pdf]

Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. Reconstructing influenza incidence by deconvolution of daily mortality time series. PNAS 106: 21825–21829 (2009) [pdf]

Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLoS Genetics 4: 1000304 (2008) [pdf]

Dushoff J, Plotkin JB, Levin SA, Earn DE. Dynamical resonance can explain the seasonality of influenza incidence. PNAS 101: 16915-16916 (2004) [pdf]

Plotkin JB, Robins H, Levine A. Tissue-specific codon usage and the expression of human genes. PNAS 101: 12588-12591 (2004) [pdf]

Plotkin JB, Dushoff J, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428: 942-945 (2004) [pdf]

Plotkin JB, Dushoff J. Codon bias and frequency-dependent selection on the hemagglutinin epitopes of Influenza A virus. PNAS 100: 7152-7157 (2003) [pdf]

Plotkin JB, Dushoff J, Levin SA. Hemagglutinin sequence clusters and the antigenic evolution of Influenza A virus. PNAS 99: 6263-6268 (2002) [pdf]

Krakauer D, Plotkin JB. Redundancy, anti-redundancy, and the stability of genomes. PNAS 99: 1405-1409 (2002) [pdf]

Plotkin JB, Potts M, Yu D, Bunyavejchewin S, Condit R, Foster R, Hubbell S, LaFrankie J, Manokaran N, Seng L, Sukumar R, Nowak MA, Ashton PS. Predicting species diversity in tropical forests. PNAS 97: 10850-10854 (2000) [pdf]

Nowak M, Plotkin JB, Jansen V. The evolution of syntactic communication. Nature 404: 495-498 (2000) [pdf]