Peter R. Wilton

I am a computational biologist and population geneticist, working to turn observations of genetic variation within populations into insights about evolutionary and demographic history. Currently I am a postdoc with Rasmus Nielsen in the Departments of Integrative Biology and Statistics at UC Berkeley.

You can reach me at

I am currently employing population genetics to study mitochondrial heteroplasmy, a term for the occurrence of multiple mitochondrial genotypes within an individual. The mitochondria transmitted between mother and offspring—and those within an individual—can be thought of as a network of populations of mitochondria related by an ontogenetic phylogeny. Each branch of this phylogeny represents a different stage of life, during which the relative frequencies of different mitochondrial genotypes can change.

Adapting approaches used in population phylogenetics, I am developing methods that use heteroplasmy frequencies in different tissues to generate insight into the ontogenetic dynamics of mitochondrial inheritance and proliferation. This project is a collaboration with Kateryna Makova at Penn State University, whose lab has generated a large dataset of heteroplasmy frequencies in multiple tissues of related human individuals.

Previously, as a graduate student with John Wakeley at Harvard University's Department of Organismic and Evolutionary Biology, I studied various topics in theoretical population genetics, mostly related to the coalescent process. These topics included


Wilton, P., Zaidi, A., Makova, K., and Nielsen, R. A population phylogenetic view of mitochondrial heteroplasmy. Genetics, 2018. (bioRxiv)

Ng, N.S.R., Wilton, P.R., Prawiradilaga, D.M., Tay, Y.C., Indrawan, M., Garg, K.M., and Rheindt, F.E. The effects of Pleistocene climate change on biotic differentiation in a montane songbird clade from Wallacea. Molecular Phylogenetics and Evolution, 2017.

Wilton, P.R., Baduel, P., Landon, M.M., and Wakeley, J. Population structure and coalescence in pedigrees: comparisons to the structured coalescent and a framework for inference. Theoretical Population Biology, 2017. (bioRxiv)

Wakeley J., Wilton P.R. Coalescent and models of identity by descent. In: Encyclopedia of Evolutionary Biology. Vol 1. Academic Press, Oxford, 2016: pp. 287-292. (pdf)

Wakeley, J., King, L., and Wilton, P.R. Effects of the population pedigree on genetic signatures of historical demographic events. PNAS, 2016.

Palamara, P.F., Francioli, L., Wilton, P.R., Genovese, G., Gusev, A., Finucane, H., Sankararaman, S., Sunyaev, S., Debakker, P., Wakeley, J., Pe'er, I., Price, A.L. Leveraging distant relatedness to quantify human mutation and gene conversion rates. American Journal of Human Genetics 2015. (bioRxiv)

Wilton, P.R., Carmi, S., and Hobolth, A. The SMC’ is a highly accurate approximation to the ancestral recombination graph. Genetics 2015. (arXiv)

Rheindt, F.E., Prawiradilaga, D.M., Suparno, S., Ashari, H., and Wilton, P.R. New and significant island records, range extensions and elevational extensions of birds in eastern Sulawesi, its nearby satellites, and Ternate. Treubia 2014.

Carmi, S., Wilton, P.R., Wakeley, J., and Pe’er, I. A renewal theory approach to IBD sharing. Theoretical Population Biology 2014. (arXiv)

Rheindt, F.E., Fujita, M.K., Wilton, P.R., Edwards, S.V., 2014. Introgression and phenotypic assimilation in Zimmerius flycatchers (Tyrannidae): Population genetic and phylogenetic inferences from genome-wide SNPs. Systematic Biology 2014.

Wilton, P.R., Sloan, D.B., Logsdon Jr, J.M., Doddapaneni, H., and Neiman, M. Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum). Molecular Ecology Resources 2013.

Neiman, M., Larkin, K., Thompson, A.R., and Wilton, P. Male offspring production by asexual Potamopyrgus antipodarum, a New Zealand snail. Heredity 2012.

Willacker, J.J., von Hippel, F.A., Wilton, P.R., and Walton, K.M. Classification of threespine stickleback along the benthic–limnetic axis. Biological Journal of the Linnean Society 2010.

See also my Google Scholar profile and my PhD dissertation.


Infer dynamics of mitochondrial heteroplasmy throughout many life stages using population genetics and phylogenetics.
Simulates coalescence through randomly-generated population pedigrees. Coalped can accommodate variable population sizes, multiples demes, variable migration rates, and other features. It can produce coalescence-time distributions and infinite-alleles and infinite-sites mutation data in a variety of formats.
Infinite-sites likelihood calculator
Calculates sampling probabilities under the infinite-sites mutation model without recombination in a single- or two-deme setting. Uses the algorithm of Wu (2010).


Statistics for Biology (Fall 2014)
I was a teaching assistant for OEB 153, Statistics for Biology. For the course I created a sequence of biology-flavored labs introducing the R statistical computing environment. The labs are available on GitHub.
Coalescent Theory (Fall 2012, Fall 2015)
I was a teaching assistant for OEB 252, Coalescent Theory, a graduate-level course.


Available here.

Interactive Wright-Fisher process

An experiment with JavaScript—try it here.

Last updated Jan 2018