John Wakeley

Professor and Chair
Department of Organismic & Evolutionary Biology
telephone: (617) 495-1564
fax: (617) 384-5874


Fundamentally, my research is about extracting information from population samples of DNA sequences. More specifically, I use mathematical models to understand how a variety of current and historical factors conspire to produce the patterns of variation which are readily observable among individuals within species. I employ both analytical and computational techniques to make inferences about these factors from patterns of genetic variation.

The field I work in is called Theoretical Population Genetics. Follow this publications link for a list of references and articles to download for your fair use. These articles cover a number of topics, mainly in the sub-field of Theoretical Population Genetics called Coalescent Theory in which the objects of study are patterns of ancestral genetic relationships, or gene genealogies. You will find a bunch of articles about the genetics of subdivided populations with restricted migration, but also a number about populations in which one or a few individuals can have very large numbers of offspring, and one about a problem that has been overlooked in Coalescent Theory: that all loci in the genome have been transmitted through a single population pedigree. I sincerely hope you enjoy reading these. If you have any questions, please get in touch with me by email at the address above.

Most of this work has been supported by grants from the National Science Foundation and the National Institutes of Health. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF or the NIH.


Currently I teach OEB 153: Statistics for Biology, OEB 252: Coalescent Theory, and OEB 253r: Seminar in Evolutionary Genetics. Beginning in Fall 2013, I will also teach Freshman Seminar 24q: Evolution, Buddhism, and Ethics. You can read descriptions of them here.

I wrote a textbook on Coalescent Theory. You can find it at or at Roberts & Company Publishers. Take note of the errata sheet available at the bottom of that page, or here.


If you like Mark Rothko paintings, this is "Orange and Yellow" from 1956. This scan is by Mark Harden. Go to his site for more and, especially, to read about copyright laws and the fair use of artistic images.

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