Early Education: Philadelphia public schools, Central High School
B. S. (Honors) Zoology, University of Wisconsin, Madison, Wisconsin, 1964
National Institutes of Health Trainee (Genetics Training Grant), University of Chicago, 1964 - 1967
Ph. D., Department of Zoology, University of Chicago, 1968
National Institutes of Health Postdoctoral Research Fellow, Institute of Animal Genetics, University of Edinburgh, Edinburgh, Scotland, 1967 - 1968

Assistant Professor, Department of Genetics, University of Washington, Seattle, Washington 1967 - 1973 (on leave 1967-1968)
Associate Professor, Department of Genetics, University of Washington, Seattle, Washington, 1973 - 1978
Professor, Department of Genetics, University of Washington, Seattle, Washington, 1978-2001
Professor, Department of Genome Sciences, University of Washington, Seattle, Washington, 2001-2017
Professor Emeritus, Department of Genome Sciences, University of Washington, Seattle, Washington, 2018-present
Adjunct Professor, Department of Statistics, University of Washington, Seattle, Washington, 1981 - 2017
Adjunct Professor, Department of Zoology, University of Washington, Seattle, Washington, 1990 - 2002
Professor, Department of Zoology, University of Washington, Seattle, Washington, 2002-2003 (on joint basis with Genome Sciences)
Professor, Department of Biology, University of Washington, Seattle, Washington, 2003-2017 (on joint basis with Genome Sciences)
Adjunct Professor, Department of Computer Science and Engineering, University of Washington, Seattle, Washington 2003-2017
Sabbatical leave at Department of Genetics, University of Edinburgh, Edinburgh, Scotland, June 1982 - June 1983

Associate Editor, Genetics, June - December, 1974
Associate Editor, Theoretical Population Biology, January, 1975 - December, 1986, January, 1995 - December, 1998, January, 2003 - present
Associate Editor, Evolution, January, 1978 - December, 1979, and January, 1981 - December, 1983
Associate Editor, Journal of Classification, January, 1984 - Ausgust, 2015
Member of editorial committee, Annual Review of Ecology and Systematics, January 1982 - December, 1986
Vice President II, Society for the Study of Evolution, 1986
Member, Society for the Study of Evolution, committee to nominate an editor for Evolution, 1988
Associate, Program in Evolutionary Biology, Canadian Institute for Advanced Research, 1988-2007. Member of Advisory committee of program, 2002-2004, Chair of Advisory committee, 2005-2007.
Member, NIH NIGMS Genbank Advisory Committee, 1989 - 1993
Member, International Advisory Committee for Nucleic Acid Sequence Databases, 1991 - 1993
Member of editorial board, Molecular Phylogenetics and Evolution, January 1992 - present
Member of editorial board, Journal of Molecular Evolution, January 1993 - present
President, Society for the Study of Evolution, 1993 (President-Elect, 1992, Retiring President, 1994).
Member of editorial board, Journal of Computational Biology, January 1994 - present
Coordinator, Program in Computational Molecular Biology, University of Washington, September 2001 - September 2006. Honorary member of editorial board, Evolutionary Bioinformatics, September, 2005 - present
Member, Washington State Academy of Sciences, 2008 - present
President-Elect, Society of Molecular Biology and Evolution, 2014 (President, 2015; Former President, 2016)
Member of editorial board, Genome Biology and Evolution, 2014 - 2019

Elected to membership, American Academy of Arts and Sciences, 1992
Sewall Wright Award, American Society of Naturalists, 1993 (a biographical sketch of me by Monty Slatkin appeared in American Naturalist in January, 1995). (JSTOR)
Elected to membership, National Academy of Sciences, 1999
Weldon Memorial Prize, University of Oxford, 2000
President's Award for Excellence in Systematics, Society of Systematic Biology, 2002
Honorary degree of Doctor of Science, University of Edinburgh, 2005
Darwin-Wallace Medal, Linnean Society of London, 2009
John J. Carty Award for the Advancement of Science, National Academy of Sciences, 2009
Distinguished Scientist Award, American Institute of Biological Sciences, 2009
International Prize for Biology, Japan Society for the Promotion of Science, 2013
Friend of Darwin Award, National Center for Science Education, 2020

Links marked (JSTOR) are to versions of these papers in the JSTOR system, which can be accessed by web if your institution has a subscription to JSTOR. If they do not, by appropriately registering with JSTOR, you can read up to 6 articles per month there. Other papers available electronically as PDFs or as HTML are indicated by (PDF) or (HTML). The ones that are free are indicated. Access to the other ones will depend on your institution's electronic subscriptions. If one that is designated as "free" turns out not to be, please let me know.

1. (R. C. Lewontin and J. Felsenstein) 1965. The robustness of homogeneity tests in 2 x N tables. Biometrics 21 (1): 19-33. (JSTOR)
2. 1965. The effect of linkage on directional selection. Genetics 52 (2): 349-363. (free PDF)
3. (Walter F. Bodmer and Joseph Felsenstein) 1967. Linkage and selection: theoretical analysis of the deterministic two locus random mating model. Genetics 57 (2): 237-265. (free PDF)
4. (James F. Crow and Joseph Felsenstein) 1968. The effect of assortative mating on the genetic composition of a population. Eugenics Quarterly 15 (2): 85-97. (PDF) doi:10.1080/19485565.1968.998776 (A note on this paper and eugenics)
5. 1971. On the biological significance of the cost of gene substitution. American Naturalist 105 (1): 1-11. (JSTOR)
6. (Arno Motulsky, George R. Fraser, and Joseph Felsenstein) 1971. Public health and long-term genetic implications of intrauterine diagnosis and selective abortion. Birth Defects - Original Article Series 7 (5): 22-32.
7. 1971. Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 68 (4): 581-597. (free PDF)
8. 1971. The rate of loss of multiple alleles in finite haploid populations. Theoretical Population Biology 2 (4): 391-403. (PDF)
9. 1972. The substitutional load in a finite population. Heredity 28 (1): 57-69. (free PDF)
10. 1973. Maximum likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics 25 (5): 471-492. (free PDF)
11. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22 (3): 240-249. (JSTOR)
12. 1974. Uncorrelated genetic drift of gene frequencies and linkage disequilibrium in some models of linked overdominant polymorphisms. Genetical Research 24 (3): 281-294. (PDF)
13. 1974. The evolutionary advantage of recombination. Genetics 78 (2): 737-756. (free PDF)
14. 1975. A pain in the torus: some difficulties with models of isolation by distance. American Naturalist 109 (967): 359-368. (JSTOR)
15. 1975. (Glenn Sharrock and Joseph Felsenstein). Finding all monothetic subsets of a taxonomic group. Systematic Zoology 24 (3): 373-377. (JSTOR)
16. 1975. Genetic drift in clines which are maintained by migration and natural selection. Genetics 81 (1): 191-207. (free PDF)
17. 1976. (Joseph Felsenstein and Shozo Yokoyama). The evolutionary advantage of recombination. II. Individual selection for recombination. Genetics 83 (4): 845-859 (Corrigendum in vol. 85 (2) p. 372 1977). (free PDF) (free PDF of Corrigendum)
18. 1976. (U. Francke, J. Felsenstein, S. M. Gartler, B. R. Migeon, J. Dancis, J. E. Seegmiller, B. Bakay, and W. L. Nyhan). The occurrence of new mutants in the X-linked recessive Lesch-Nyhan disease. American Journal of Human Genetics 28 (2): 123-137 (Erratum, vol. 28, number 3, p. 311). (PDF) (free PDF of Erratum)
19. 1976. The theoretical population genetics of variable selection and migration. Annual Review of Genetics 10: 253-280. (PDF)
20. 1977. (U. Francke, J. Felsenstein, S. M. Gartler, W. L. Nyhan, and J. E. Seegmiller). Answer to criticism of Lalouel and Morton. American Journal of Human Genetics 29 (3): 307-310. (free PDF)
21. 1977. Multivariate normal genetic models with a finite number of loci. pp. 227-245 in Proceedings of the International Conference on Quantitative Genetics, August 16-21, 1976. edited by E. Pollak, O. Kempthorne, and T. B. Bailey, Jr., Iowa State University Press, Ames, Iowa. (PDF)
22. 1978. Macroevolution in a model ecosystem. American Naturalist 112 (983): 177-195. (JSTOR)
23. 1978. (Shozo Yokoyama and Joseph Felsenstein). Kin selection in an altruistic trait considered as a quantitative character. Proceedings of the National Academy of Sciences, USA 75 (1): 420-422. (JSTOR)
24. 1978. The number of evolutionary trees. Systematic Zoology 27 (1): 27-33 (Correction, vol. 30, number 1, p. 122, 1981) (JSTOR) (JSTOR of Correction) (PDF at journal) doi:10.2307/2412810
25. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27 (4): 401-410. (JSTOR) doi:10.2307/2412923 (PDF) doi:10.1093/sysbio/27.4.401 (Also reprinted as pp. 663-674 in Conceptual Issues in Evolutionary Biology, An Anthology, edited by Elliott Sober, MIT Press, Cambridge, Massachusetts, 1984.)
26. 1979. Alternative methods of phylogenetic inference and their interrelationship. Systematic Zoology 28 (1): 49-62. (JSTOR) doi:10.2307/2412998 (PDF) doi:10.1093/sysbio/28.1.49
27. 1979. r- and K-selection in a completely chaotic population model. American Naturalist 113 (4): 499-510. (JSTOR) (PDF) doi:10.1086/283409
28. 1979. Isolation by distance: reply to Lalouel and Morton. Annals of Human Genetics 42 (4): 523-527. (PDF) doi: 10.1111/j.1469-1809.1979.tb00685.x
29. 1979. A mathematically tractable family of genetic mapping functions with different amounts of interference. Genetics 91 (4): 769-775 (Corrigendum, vol. 92, number 2, p. 685). (free PDF) (free PDF of Corrigendum)
30. 1979. Excursions along the interface between disruptive and stabilizing selection. Genetics 93 (3): 773-795. (free PDF)
31. 1981. Skepticism towards Santa Rosalia, or Why are there so few kinds of animals? Evolution 35 (1): 124-138. (JSTOR) (free PDF) doi:10.2307/2407946
32. 1981. Bibliography of Theoretical Population Genetics. Dowden, Hutchinson, and Ross, Stroudsburg, Pennsylvania. (download bibliography)
33. 1981. (Stanley Sawyer and Joseph Felsenstein). A continuous migration model with stable demography. Journal of Mathematical Biology 11 (2): 193-205. (PDF) doi:10.1007/BF00275442
34. 1981. Continuous-genotype models and assortative mating. Theoretical Population Biology 19 (3): 341-357. (PDF) doi:10.1016/0040-5809(81)90025-3
35. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17 (6): 368-376. (PDF) (free PDF) doi:10.1007/BF01734359
36. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnean Society 16 (3): 183-196. (free PDF) doi:10.1111/j.1095-8312.1981.tb01847.x
37. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35 (6): 1229-1242. (JSTOR) (free PDF) doi:10.2307/240813
38. 1982. (J. Felsenstein, S. Sawyer, and R. Kochin). An efficient method for matching nucleic acid sequences. Nucleic Acids Research 10 (1): 133-139. (free PDF) (free HTML and PDF from Oxford Univ. Press) doi:10.1093/nar/10.1.133
39. 1982. How can we infer geography and history from gene frequencies? Journal of Theoretical Biology 96 (1): 9-20. (free PDF)
40. 1982. Numerical methods for inferring evolutionary trees. Quarterly Review of Biology 57 (4): 379-404. (PDF) (JSTOR) doi:10.1086/412935
41. 1983. (S. Sawyer and J. Felsenstein). Isolation by distance in a hierarchically clustered population. Journal of Applied Probability 20 (1): 1-10. (JSTOR) (PDF) doi:10.2307/3213715
42. 1983. Inferring evolutionary trees from DNA sequences. pp. 133-150 in Statistical Analysis of DNA Sequence Data, edited by B. S. Weir. M. Dekker, New York.
43. 1983. (editor) Numerical Taxonomy: Proceedings of a NATO Advanced Study Institute. NATO Advanced Study Institute Series G (Ecological Sciences), No. 1. Springer-Verlag, Berlin, Heidelberg, and New York. (Springer Link). doi:10.1007/978-3-642-69024-2
44. 1983. Methods for inferring phylogenies: a statistical view. pp. 315-334 in Numerical Taxonomy: Proceedings of a NATO Advanced Study Institute, edited by J. Felsenstein. NATO Advanced Study Institute Series G (Ecological Sciences), No. 1. Springer-Verlag, Berlin, Heidelberg, and New York. (PDF) doi:10.1007/978-3-642-69024-2_35
45. 1983. Computers in systematics: one perspective. pp. 590-609 in Numerical Taxonomy: Proceedings of a NATO Advanced Study Institute, edited by J. Felsenstein. NATO Advanced Study Institute Series G (Ecological Sciences), No. 1. Springer-Verlag, Berlin, Heidelberg, and New York. (PDF) doi:10.1007/978-3-642-69024-2_69
46. 1983. Statistical inference of phylogenies. Journal of the Royal Statistical Society, Series A (General) 146: 246-272. (JSTOR)).
47. 1983. Parsimony in systematics: biological and statistical issues. Annual Review of Ecology and Systematics 14: 313-333. (JSTOR). doi.org/10.1146/annurev.es.14.110183.001525
48. 1984. Distance methods for inferring phylogenies: a justification. Evolution 38: 16-24. (JSTOR) (free PDF) doi:10.2307/2408542
49. 1984. The statistical inference approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. pp. 169-191 in Cladistics: perspectives on the reconstruction of evolutionary history, edited by T. Duncan and T. F. Stuessy. Columbia University Press, New York.
50. 1985. Phylogenies and the comparative method. American Naturalist 125 (1): 1-15. (JSTOR) (PDF) doi:10.1086/284325
51. 1985. Recombination and sex: is Maynard Smith necessary? pp. 209-219 in Evolution: Essays in honour of John Maynard Smith, edited by P. J. Greenwood, P. H. Harvey, and M. Slatkin. Cambridge University Press, Cambridge.
52. 1985. Confidence limits on phylogenies with a molecular clock. Systematic Zoology 34 (2): 152-161. (JSTOR) (PDF) doi:10.2307/2413323
53. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (4): 783-791. (JSTOR) (PDF) doi:10.2307/2408678
54. 1985. Phylogenies from gene frequencies: a statistical problem. Systematic Zoology 34 (3): 300-311. (JSTOR) (PDF) doi:10.2307/2413149
55. 1986. Distance methods: reply to Farris. Cladistics 2 (2): 130-143. (PDF) doi:10.1111/j.1096-0031.1986.tb00448.x
56. 1986. Population differences in quantitative characters and gene frequencies: a comment on papers by Lewontin and Rogers. American Naturalist 127 (5): 731-732. (JSTOR)
57. (Felsenstein, J. and E. Sober). 1986. Parsimony and likelihood: an exchange. Systematic Zoology 35 (4): 617-626. (JSTOR) (PDF) doi:10.2307/2413121
58. (Cavender, J. A. and J. Felsenstein). 1987. Invariants of phylogenies in a simple case with discrete states. Journal of Classification 4 (1): 57-71. (free PDF) doi:10.1007/BF01890075
59. 1987. Sex and the evolution of recombination. pp. 74-86 in The Evolution of Sex, An Examination of Current Ideas, edited by R. E. Michod and B. R. Levin. Sinauer Associates, Sunderland, Massachusetts.
60. 1987. Estimation of hominoid phylogeny from a DNA hybridization data set. Journal of Molecular Evolution 26 (1): 123-131. (PDF) doi:10.1007/BF02111286
61. 1988. The detection of phylogeny. pp. 112-127 in Prospects in Systematics, edited by D. L. Hawksworth. Systematics Association, London.
62. 1988. Perils of molecular introspection (News and Views). Nature 335 (8 September 1988): 118-119. (free PDF) doi:10.1038/335118a0
63. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19: 445-471. (free PDF)
64. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 22: 521-565. (free PDF) doi:10.1146/annurev.ge.22.120188.002513
65. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5 (2): 164-166. (PDF (maybe)) doi:10.1111/j.1096-0031.1989.tb00562.x
66. 1989. Alan Robertson's contributions to population genetics. pp. 3-11 in Evolution and Animal Breeding. Reviews on Molecular and Quantitative Approaches in Honour of Alan Robertson, edited by W. G. Hill and T. F. C. MacKay. C. A. B. International, Wallingford, U.K.
67. 1990. (Golding, B. and J. Felsenstein). A maximum likelihood approach to the detection of selection from phylogeny. Journal of Molecular Evolution 31 (6): 511-523. (PDF) doi:10.1007/BF02102078
68. 1991. (J. L. Thorne, H. Kishino and J. Felsenstein). An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution 33 (2): 114-124. (PDF) doi:10.1007/BF02193625
69. 1991. Counting phylogenetic invariants in some simple cases. Journal of Theoretical Biology 152 (3): 357-376. (free PDF) doi:10.1016/S0022-5193(05)80200-0
70. 1991. Allan Charles Wilson (1934-1991). Nature 353 (5 September 1991): 19. (free PDF) doi:10.1038/353019a0
71. 1992. (J. L. Thorne, H. Kishino and J. Felsenstein). Inching toward reality: an improved likelihood model of sequence evolution. Journal of Molecular Evolution 34 (1): 3-16. (PDF) doi:10.1007/BF00163848
72. 1992. Phylogenies from restriction sites: a maximum likelihood approach. Evolution 46 (1): 159-173. (JSTOR)
73. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genetical Research 59 (2): 139-147. (PDF) doi:10.1017/S0016672300030354
74. 1992. Estimating effective population size from samples of sequences: a bootstrap Monte Carlo approach. Genetical Research 60 (3): 209-220. (PDF) doi:10.1017/S0016672300030962
75. 1993. (Archie, J. and J. Felsenstein). The number of evolutionary steps on random and minimum length trees for random evolutionary data. Theoretical Population Biology 43 (1): 52-79. (free PDF) doi:10.1006/tpbi.1993.1003
76. 1993. (J. Felsenstein and H. Kishino). Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42 (2): 193-200. (JSTOR) (PDF) doi: 10.1093/sysbio/42.2.193
77. 1994. (M. K. Kuhner and J. Felsenstein). A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11 (3): 459-468 (Erratum 12 (3): 525 (1995). (free PDF) (free PDF of erratum) doi.org/10.1093/oxfordjournals.molbev.a040126
78. 1995. (M. K. Kuhner, J. Yamato, and J. Felsenstein). Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140 (4): 1421-1430. (free PDF)
79. 1996. (J. Felsenstein and G. A. Churchill). A hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13 (1): 93-104. (free PDF) doi.org/10.1093/oxfordjournals.molbev.a025575
80. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. pp. 418-427 in Computer Methods for Macromolecular Sequence Analysis, edited by R. F. Doolittle. Methods in Enzymology, vol. 266. Academic Press, Orlando, Florida. (PDF) doi:10.1016/S0076-6879(96)66026-1
81. 1996. (Swofford, D. L., J. L. Thorne, J. Felsenstein, and B. M. Wiegmann). The topology-dependent permutation test for monophyly does not test for monophyly. Systematic Biology 45 (4): 573-577. (free PDF) DOI: 10.2307/2413533
82. 1997. (M. K. Kuhner, J. Yamato, and J. Felsenstein). Applications of Metropolis-Hastings genealogy sampling. pp. 183-192 in Progress in Population Genetics and Human Evolution, edited by P. Donnelly and S. Tavare. IMA Volumes in Mathematics and its Applications, volume 87. Springer Verlag, Berlin.
83. 1997. Population differentiation and evolutionary processes. pp. 31-43 in Genetic Effects of Straying of Non-Native Hatchery Fish into Natural Populations, edited by W. Stewart Grant. NOAA Technical Memorandum NMFS-NWFSC-30. U. S. Department of Commerce. (The complete text and figures are also available on the Web at
    https://www.nwfsc.noaa.gov/publications/scipubs/techmemos/tm30/felsenstein.html
84. 1997. An alternating least squares approach to inferring phylogenies from pairwise distances. Systematic Biology 46 (1): 101-111. (free PDF) doi:10.2307/2413638
85. 1998. (M. K. Kuhner, J. Yamato and J. Felsenstein). Maximum likelihood estimation of population growth rates based on the coalescent Genetics 149 (1): 429-434. (free HTML) (free PDF)
86. 1999. (Rodrigo, A. G. and J. Felsenstein). Coalescent approaches to HIV population genetics. pp. 233-272 in The Evolution of HIV, edited by K. A. Crandall. Johns Hopkins University Press, Baltimore.
87. 1999. (P. Beerli and J. Felsenstein). Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152 (2): 763-773. (free HTML) (free PDF)
88. 1999. (Felsenstein, J., M. K. Kuhner, J. Yamato, and P. Beerli). 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. Selected proceedings of the Joint AMS-IMS-SIAM Summer Conference on Statistics in Molecular Biology held in Seattle, WA, June 22--26, 1997, edited by Francoise Seillier-Moiseiwitsch. IMS Lecture Notes-Monograph Series, volume 33. Institute of Mathematical Statistics and American Mathematical Society, Hayward, California. (free PDF) doi:10.1214/lnms/1215455552
89. 2000. From population genetics to evolutionary genetics: a view through the trees. pp. 609-627 in Evolutionary Genetics: From Molecules to Morphology, vol. 1, edited by R. S. Singh and C. B. Krimbas. Cambridge University Press, Cambridge.
90. 2000. (M. K. Kuhner, P. Beerli, J. Yamato, and J. Felsenstein). Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156 (1): 439-447. (free PDF)
91. 2000. Comment in discussion of paper by M. Stephens and P. Donnelly "Inference in molecular population genetics," Journal of the Royal Statistical Society, Series B 62 (4): 605-655 (comment is on page 645). (JSTOR) (free PDF) doi:10.1111/1467-9868.00254
92. 2000. (Kuhner, M. K. and J. Felsenstein). Sampling among haplotype resolutions in a coalescent-based genealogy sampler. Genetic Epidemiology 19 (Supplement 1): S15-S21. (PDF)
93. 2000. (Kuhner, M. K., J. Yamato and J. Felsenstein). Maximum likelihood estimation of recombination rates from population data. Genetics 156 (1): 1393-1401. (free HTML) (free PDF)
94. 2001. (Beerli, P. and J. Felsenstein). Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, USA 98 (8): 4563-4568. (free HTML) (free PDF) doi.org/10.1073/pnas.081068098
95. 2001. The troubled growth of statistical phylogenetics. Systematic Biology 50 (4): 465-467. (free PDF) doi.org/10.1080/10635150119297
96. 2001. Taking variation of evolutionary rates between sites into account in inferring phylogenies. Journal of Molecular Evolution 53 (4): 447-455. (PDF) doi:10.1007/s002390010234
97. 2002. Quantitative characters, phylogenies, and morphometrics. pp. 27-44 in Morphology, Shape, and Phylogenetics, edited by N. MacLeod. Systematics Association Special Volume Series 64. Taylor and Francis, London.
98. 2002. Contrasts for a within-species comparative method. pp. 118-129 in Modern Developments in Theoretical Population Genetics: The Legacy of Gustave alecot, edited by M. Slatkin and M. Veuille. Oxford University Press, Oxford.
99. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.
100. 2005. Using the quantitative genetic threshold model for inferences between and within species. Philosophical Transactions of the Royal Society of London, Series B 360 (1459): 1427-1434. (HTML) (PDF) doi:10.1098/rstb.2005.1669
101. 2006. Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci? Molecular Biology and Evolution 23 (3): 691-700. (free HTML) (free PDF) doi:10.1093/molbev/msj079
102. 2007. Trees of genes in populations. pp. 3-29 in Reconstructing Evolution. New Mathematical and Computational Advances, ed. O. Gascuel and M. Steel. Clarendon Press, Oxford.
103. 2007. Has natural selection been refuted? The arguments of William Dembski. Reports of the National Center for Science Education 27 (3-4): 20-26. (free HTML)
104. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171 (6): 713-725. (HTML) (PDF) doi:10.1086/587525
105. (A. RoyChoudhury, J. Felsenstein, and E. A. Thompson). 2008. A two-stage pruning algorithm for likelihood computation for a population tree. Genetics 180 (2): 1095-1105. (free HTML) (free PDF) doi:10.1534/genetics.107.085753
106. 2008. Bootstrap confidence levels for phylogenetic trees. pp. 336-337 in The Science of Bradley Efron. Selected Papers, ed. C. N. Morris and R. Tibshirani. Springer Series in Statistics: Perspectives in Statistics. Springer, New York.
107. (Emery L. S., J. Felsenstein, and J. M. Akey). 2010. Estimators of the human effective sex ratio detect sex biases on different timescales. American Journal of Human Genetics 87 (6): 848-56 (Epub 2010 Nov 25). (free HTML) (free PDF) doi:10.1016/j.ajhg.2010.10.021
108. (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. (free PDF) (free HTML) doi:10.1098/rstb.2010.0311
109. 2012. A comparative method for both discrete and continuous characters using the threshold model. American Naturalist 179 (2): 145-156. (PDF) (HTML) doi:10.1086/663681
110. (Bryant D., R. Bouckaert, J. Felsenstein, N. A. Rosenberg, A. RoyChoudhury). 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 29 (8): 1917-1932. (free PDF) (free HTML) doi:10.1093/molbev/mss086
111. 2015. Covariation of gene frequencies in a stepping-stone lattice of populations. Theoretical Population Biology 100: 88-97. (HTML) (free HTML) (PDF) (free PDF) doi:10.1016/j.tpb.2014.12.004
112. (Leache, A. D., B. L. Banbury, J. Felsenstein, A. Nieto-Montes de Oca, and A. Stamatakis). 2015. Short tree, long tree, right tree, wrong tree: New acquisition bias corrections for inferring SNP phylogenies. Systematic Biology 64 (6): 1032-1047. (free PDF) (free HTML) doi:10.1093/sysbio/syv053
113. 2018. Anthony Edwards, Luca Cavalli-Sforza, and phylogenies. pp. 325-333 in Phylogenetic Inference, Selection Theory, and History of Science. Selected Papers of A.W.F. Edwards, with Commentaries, ed. Rasmus Grønfeldt Winther. Cambridge University Press, Cambridge, U.K. doi:10.1017/9781316276259
114. 2022. Luca Cavalli-Sforza and phylogenetic evolutionary methods. Human Population Genetics and Genomics, Special Issue: Luca Cavalli-Sforza’s legacy, 100 years after his birth, ed. Guido Barbujani and Lounes Chikhi. 2 (3): 0004 doi:10.47248/hpgg2202030004

1. 1968. Effects of linkage and epistasis on fixation probabilities. Proceedings of the XII International Congress of Genetics, Volume II, p. 145.
2. 1969. The effective size of a population with overlapping generations. Genetics 61: s18.
3. 1971. The evolutionary advantage of recombination. Genetics 68: s19 .
4. 1973. Estimation of number of loci controlling variation in a quantitative character. Proc. 13th International Congress of Genetics. Genetics 74: (2, part 2) s79.
5. 1975. The relationship between theory and data in population genetics. Genetics 80: s4.
6. 1975. Discussion of preceding papers. pp. 106-131 in Proceedings of the Eighth International Conference on Numerical Taxonomy, edited by G. F. Estabrook. W. H. Freeman, San Francisco.
7. 1984. Confidence limits on most parsimonious phylogenies under a molecular clock. Genetics 107: s31.
8. 1999. Coalescents, phylogenies and likelihoods. Biological Bulletin 196: 343-344. (free PDF)

1. 1971. Population theory (Review of Mathematical Topics in Population Genetics, ed K. Kojima). Science 171: 562. (JSTOR))
2. 1972. Reply to Turner's letter. American Naturalist 106: 672. (JSTOR)
3. 1972. Review of Theoretical Aspects of Population Genetics , by M. Kimura and T. Ohta. Quarterly Review of Biology 47: 333-334. (JSTOR)
4. 1972. Review of A Primer of Population Biology, by E. O. Wilson and W. H. Bossert. American Journal of Human Genetics 24: 607-608. (free PDF)
5. 1972. Review of Probability Models and Statistical Methods in Genetics, by R. C. Elandt-Johnson. American Journal of Human Genetics 24: 357. (free PDF)
6. 1973. Review of The Assessment of Population Affinities in Man, edited by J. S. Weiner and J. Huizinga. American Journal of Human Genetics 25: 459-460. (free PDF)
7. 1973. Review of Polymorphisms with Linked Loci, by V. Arunachalam and A. R. G. Owen. Quarterly Review of Biology 48: 30. (JSTOR)
8. 1974. Review of Numerical Taxonomy, by P. H. A. Sneath and R. R. Sokal. American Scientist 62: 602.
9. 1974. Population Genetics from France. (Review of The Genetic Structure of Populations, by A. Jacquard). Science 186: 1028. (JSTOR)
10. 1975. Review of Genetic Structure of Populations, edited by N. E. Morton. American Journal of Human Genetics 27: 125-126. (free PDF)
11. 1975. Review of The Genetic Basis of Evolutionary Change, by R. C. Lewontin. Evolution 29: 587-590. (JSTOR)
12. 1976. Review of Molecular Population Genetics and Evolution, by M. Nei. American Journal of Human Genetics 28: 303-304. (free PDF)
13. 1977. Review of First Course in Population Genetics, by C. C. Li. Quarterly Review of Biology 52: 410-411. (JSTOR)
14. 1977. Review of Human Evolutionary Trees, by E. A. Thompson. Quarterly Review of Biology 52: 231. (JSTOR)
15. 1978. Review of Evolution, by Theodosius Dobzhansky, Francisco J. Ayala, G. Ledyard Stebbins, and James W. Valentine. American Scientist 66: 225-226.
16. 1979. Quantitative genetics (review of Quantitative Genetic Variation, ed, James N. Thompson and J. M. Thoday). Science 206: 549. (JSTOR)
17. 1980. A view of population genetics (review of Mathematical Population Genetics, by Warren J. Ewens). Science 208: 1253. (JSTOR)
18. 1981. Review of The Geometry of Population Genetics, by Ethan Akin. Quarterly Review of Biology 56: 76. (JSTOR)
19. 1982. A theme that will be repeated (review of Evolution and Variation in Multigene Families, by Tomoko Ohta). Evolution 36: 206.
20. 1982. Review of The Mathematical Theory of Quantitative Genetics, by M.G. Bulmer. Quarterly Review of Biology 57: 68. (JSTOR)
21. 1983. Another beacon in the fog (review of Phylogenetics: The Theory and Practice of Phylogenetic Systematics, by E. O. Wiley). Quarterly Review of Biology 58: 60-62. (JSTOR)
22. 1983. Review of Evolution in Age-Structured Populations by B. Charlesworth. Biometrics 39: 818-819.
23. 1984. Comparatively better (review of The Explanation of Organic Diversity: The Comparative Method and Adaptations for Mating, by Mark Ridley). Nature 308: 565.
24. 1985. Review of Genetics of Populations, by Philip W. Hedrick. Quarterly Review of Biology 60: 77-78. (JSTOR)
25. 1986. Waiting for Post-Neo-Darwin (review of Evolutionary Theory: Paths into the Future by J. W. Pollard). Evolution 40: 883-889. (JSTOR)
26. 1986. Evolution in the twentieth century (review of Sewall Wright and Evolutionary Biology by W. B. Provine, and Evolution - Selected Papers by Sewall Wright). Nature 324: 175-176.
27. 1986. Review of Taxonomic analysis in biology: computers, models, and databases by Lois A. Abbott, Frank A. Bisby, and David J. Rogers. Quarterly Review of Biology 61: 587. (JSTOR)
28. 1987. Access to theory (review of books by F. B. Christiansen and M. W. Feldman and by J. F. Crow). Nature 326 (6109): 219-220.
29. 1987. Comment in discussion of paper by C. F. J. Wu, Jackknife, bootstrap and other resampling methods in regression analysis. Annals of Statistics 14: 1261-1295 (comment is pp. 1304-1305). (JSTOR) (free PDF)
30. 1987. Comment (in discussion of paper by D. Barry and J. A. Hartigan). Statistical Science 2: 208-209. (JSTOR) (free PDF)
31. 1987. Molecular evolution in search of itself (review of Molecular Evolutionary Genetics by M. Nei). Cell 51: 343-344.
32. 1988. Further selection (review of A primer of population genetics, 2nd edition, by D. L. Hartl, and Population genetics: basic principles by D. P. Doolittle). Nature 332: 182.
33. 1989. Mathematics vs. evolution (review of Mathematical Evolutionary Theory, edited by Marcus W. Feldman). Science 246: 941-942. (JSTOR))
34. 1989. Data basis (review of Computational molecular biology by A. M. Lesk and Biomolecular data. A resource in transition, by R. R. Colwell). Trends in Genetics 5: 419-420.
35. 1991. Review of Reconstructing the past: parsimony, evolution, and inference by Elliott Sober. Journal of Classification 8: 122-125.
36. 1991. Review of Principles of Population Genetics, by D. L. Hartl and A. G. Clark. American Scientist 69: 464.
37. 1992. Review of Genes in Populations, by Eliot B. Spiess. American Journal of Human Genetics 51: 224. (free PDF)
38. 1992. Review of Selected Genetics Papers of J.B.S. Haldane, edited by K. R. Dronamraju. Genetical Research 60: 153-154. (free PDF)
39. 1992. Review of Proceedings of the Michigan Morphometrics Workshop, edited by F. J. Rohlf and F. L. Bookstein. Quarterly Review of Biology 67: 418-419. (JSTOR)
40. 1993. Unspoken Disagreements (review of Phylogenetic Analysis of DNA Sequences, edited by Michael M. Miyamoto and Joel Cracraft). Cladistics 8: 191-196. (PDF)
41. 2000. Comment (in discussion of paper by M. A. Stephens and P. Donnelly). Journal of the Royal Statistical Society, Series B 82 (4): 646.
42. 2004. An ancestor's influence (review of Francis Galton: Pioneer of Heredity and Biometry by Michael Bulmer). Nature Genetics 36: 1031. (HTML) (PDF)
43. 2006. What mathematicians will see of phylogenies (review of Mathematics of Evolution and Phylogenies, edited by Olivier Gascuel). Evolution 60: 872-874. (HTML) (PDF)
44. 2006. Review of Evolutionary Theory: Mathematical and Conceptual Foundations by Sean H. Rice. Quarterly Review of Biology 81: 171-172. (HTML) (PDF)
45. 2008. Bootstrap confidence levels for phylogenetic trees. Introduction. pp. 336-337 in The Science of Bradley Efron, ed. C. N. Morris, and R. Tibshirani. Introduction to Chapter 17. Springer, New York.
46. 2008. Review of Computational Molecular Evolution by Ziheng Yang. Quarterly Review of Biology 83: 205-206. (HTML)
47. 2008. Review of Introduction to Computational Biology: An Evolutionary Approach by Bernhard Haubold and Thomas Wiehe. SIAM Review 50: 390-391.
48. 2009. Coalescents in full bloom (review of Coalescent Theory: An Introduction, by John Wakeley). Evolution 63: 3275-3276.
    Computer Program Distribution

    PHYLIP, the Phylogeny Inference Package, a package of programs for inferring phylogenies, has been distributed since October 1980. The programs are distributed free on the Web. There are about 31,000 registered users (and many unregistered ones). The programs are distributed in C source code (versions before the spring of 1993 were in Pascal). with extensive documentation in computer-readable form. Other people have helped with earlier distribution of specific precompiled versions for different microcomputers (George D.F. Wilson, then in San Diego, with the DOS version, and Willem Ellis in Amsterdam with the Macintosh version).

    LAMARC, a package of programs for Likelihood Analysis by Metropolis Algorithm with Random Coalescents, is distributed by our laboratory (the central person responsible for it is Dr. Mary Kuhner). It is a series of programs in C and C++, currently 4 of them. They are distributed by by World Wide Web, for free, in source code and in Windows and Macintosh executables. The programs implement Markov Chain Monte Carlo analysis of likelihoods of population samples of nucleotide sequences, electrophoretic markers, and microsatellite data. They estimate population parameters such as the scaled effective population size, migration rates, population growth rates, and recombination rates. There are currently about 1500 registered users.

    PopG, a one-locus population genetics simulation. This was developed for my teaching. It is freely available here as a Java application. It can simulate natural selection, mutation, migration and genetic drift in up to 1000 populations of up to 100,000 individuals.

    Students Trained

    Fred Allendorf (Interdisciplinary Ph. D., jointly supervised with Frederick M. Utter, 1972)
    Michael A. Turelli (Ph. D., Biomathematics, 1977)
    Shozo Yokoyama (Ph. D., Biomathematics, 1977)
    J. Bruce Walsh (Ph. D., Genetics, 1983)
    Mark Grote (M.S., Statistics, 1990)
    Jeffrey L. Thorne (Ph. D., Genetics, 1991)
    Lindsey Dubb (Ph. D., Genome Sciences, 2005)
    Chul Joo Kang (Ph. D., Genome Sciences, 2008)
    Alice Beecher Popejoy (Ph.D., Public Health Genetics Program, 2017)
    Michael Dorrity (Ph.D., Biology, jointly supervised with Christine Queitsch, 2018)

    Postdoctoral Fellows Supervised

    Ruth Shaw, 1984-1987
    Mary Kuhner, 1993-1996
    Emília Martins, 1992-1994
    Peter Beerli, 1994-1996
    Nicolas Salamin, 2003-2004
    Lucian P. Smith (jointly with Mary K. Kuhner), 2006-2008
    Brendan O'Fallon, 2009-2011

    Current Research Grants

    None.