Papers from the Felsenstein lab

My Ph.D. Thesis

In folder thesis:

Felsenstein, J. 1968. Statistical Inference and the Estimation of Phylogenies. Ph.D. thesis, Department of Zoology, University of Chicago.

Papers in this folder

In folder invariants

Felsenstein, J. 1990. Counting phylogenetic invariants in some simple cases. Journal of Theoretical Biology 152: 357-376.

In folder restml

Felsenstein, J. 1992. Phylogenies from restriction sites: a maximum likelihood approach. Evolution 46: 159-173.

In folder ne

Felsenstein, J. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research 59: 139-147.

In folder montecarlo

Felsenstein, J. 1992. Estimating effective population size from population samples of sequences: a bootstrap Monte Carlo approach. Genetical Research 59: 139-147 (December issue).

[note – the method proposed in this paper is wrong] It has been shown to give a biased estimate of theta. The paper by Felsenstein, Yamato, and Kuhner corrects this. That paper is available here in directory metro and the program to implement it is LAMARC

In folder hillis

Felsenstein, J. and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42: 193-200 (June)

In folder simulation

Kuhner, M. K. and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11: 459-468.

In folder metro

Kuhner, M. K., J. Yamato, and J. Felsenstein. 1995. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.

In folder hmc

Felsenstein, J. and G. A. Churchill. 1996. A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution. Molecular Biology and Evolution 13: 93-104.

In folder proteins

Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. pp. 418-427 in Computer Methods for Macromolecular Sequence Analysis, ed. R. F. Doolittle. Methods in Enzymology, vol. 266. Academic Press, Orlando, Florida.

In folder ima

Kuhner, M. K., J. Yamato, and J. Felsenstein 1997. Applications of Metropolis-Hastings genealogy sampling. pp. 183-192 in Progress in Population Genetics and Human Evolution, ed. P. Donnelly and S. Tavare. IMA Volumes in Mathematics and its Applications, volume 87. Springer Verlag, Berlin.

In folder distance

Felsenstein, J. 1997. An alternating least squares approach to inferring phylogenies from pairwise distances. Systematic Biology 46: 101-111.

In folder migrate

Beerli, P. and J. Felsenstein. 1999. Maximum Likelihood estimation of migration rates and effective population numbers in two populations. Genetics 152: 763-773.

In folder ims

Felsenstein, J., M. K. Kuhner, J. Yamato, and P. Beerli. 1999. Likelihoods on coalescents: a Monte Carlo sampling approach to inferring parameters from population samples of molecular data. pp. 163-185 in Statistics in Molecular Biology and Genetics, ed. Francoise Seillier-Moiseiwitsch. IMS Lecture Notes-Monograph Series, volume 33. Institute of Mathematical Statistics and American Mathematical Society, Hayward, California.

In folder evolgen

Felsenstein, J. 2000. From population genetics to evolutionary genetics: a view through the trees. pp. 609-627 in Evolutionary Genetics: From Molecules to Morphology, ed. R. S. Singh and C. B. Krimbas. Cambridge University Press, Cambridge.

In folder snp

Kuhner, M. K., P. Beerli, J. Yamato, and J. Felsenstein. 2000. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156: 439-447.

In folder statphy

Felsenstein, J. 2001. The troubled growth of statistical phylogenetics. Systematic Biology 50: 465-467.

In folder rates

Felsenstein, J. 2001. Taking variation of evolutionary rates between sites into account in inferring phylogenies. Journal of Molecular Evolution 53: 447-455.

In folder quantchar

Felsenstein, J. 2002. Quantitative characters, phylogenies, and morphometrics.pp. 27-44 in Morphology, Shape, and Phylogenetics, ed. N. MacLeod. Systematics Association Special Volume Series 64. Taylor and Francis, London.

In folder spectrum

Felsenstein, J. 2002. Contrasts for a within-species comparative method. pp. 118-129 in Modern Developments in Theoretical Population Genetics, ed. M. Slatkin and M. Veuille. Oxford University Press, Oxford.

In folder galton

Felsenstein, J. 2004. An ancestor’s influence (review of Francis Galton: Pioneer of Heredity and Biometry, by Michael Bulmer). Nature Genetics 36 (10): 1031.

In folder threshold

Felsenstein, J. 2005. Using the quantitative genetic threshold model for inferences between and within species. Philosophical Transactions of the Royal Society of London, series B 360: 1427-1434.

In folder coalpower
Felsenstein, J. 2006. Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci? Molecular Biology and Evolution 23: 691-700.

In folder paris2005 Felsenstein, J. 2007. Trees of genes in populations. pp. 3-29 in Reconstructing Evolution. New Mathematical and Computational Advances, ed. Olivier Gascuel and Mike Steel. Clarendon Press, Oxford.

In folder comparerr

Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171: 713-725.

In folder stone

Stone, G. N., S. Nee, and J. Felsenstein. 2011. Controlling for non-independence in comparative analysis of patterns across populations within species. Philosophical Transactions of the Royal Society B 366 (1569): 1410-1424.

In folder threshold2

Felsenstein, J. 2012. A comparative method for both discrete and continuous characters using the threshold model. American Naturalist 179: 145-156.


Please note carefully that these papers, as published in the journals, are copyright to the publishers of those journals.

Note that in each case these are the final versions as submitted to the journal (the last full manuscript version) but do not reflect changes that the editor or I may have made in proof. Published quotations of these manuscripts should be based on the published version; quotations before publication should be checked with me by e-mail.

In addition, many of my older papers are available on-line in the JSTOR system which makes older academic journals available. Your institution would need to have a subscription to JSTOR for it to be available to you. Links to these papers are available in my Curriculum Vitae which is at this link

It also has links to on-line copies of some of my papers at the sites of the journals that published them. These too may require subscriptions.

Supplementary materials for earlier work

For earlier work, including earlier papers, I am making available materials including the computer programs that were used for the numerical examples. I am gradually putting more of these online.

This includes computer programs from those projects


Joe Felsenstein

felsenst (at) gmail.com

joe (at) gs.washington.edu