Pennings, P. S., S. Kryazhimskiy, and J. Wakeley. 2014. Loss and recovery of genetic diversity in adapting populations of HIV. PLoS Genet. 10(1):e1004000. (pdf)

Wakeley, J. 2013. Coalescent theory has many new branches. Theoret. Pop. Biol. 87:1-4. (pdf)

Wakeley, J., L. King, B. S. Low, and S. Ramachandran. 2012. Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescent. Genetics 190:1433-1445. (pdf)

Arnold, B., K. Bomblies, and J. Wakeley. 2012. Extending coalescent theory to autotetraploids. Genetics 192:195-204. (pdf)

Maruvka, Y. E., N. M. Shnerb, Y. Bar-Yam, and J. Wakeley, 2011. Recovering population parameters from a single genealogy: an unbiased estimator of the growth rate. Mol. Biol. Evol. 28:1617-1631. (pdf)

Watson, R. A., D. Weinreich, and J. Wakeley, 2011. Genome structure and the benefit of sex. Evolution 65:523-536. (pdf)

Wakeley, J. 2010. Natural selection and coalescent theory. Pp. 119-149 in Evolution since Darwin: The First 150 Years (Michael A. Bell, Douglas J. Futuyma, Walter F. Eanes, and Jeffrey S. Levinton eds.), Sinauer and Associates, Sunderland, Massachusetts. (pdf, long first draft) (pdf, shorter second draft) Note: neither of these is exactly what was published, so get the book.

Cenik, C. and J. Wakeley 2010. Pacific salmon and the coalescent effective population size. PLoS One 5(9):e13019. (pdf)

Garrigan, D., R. Lewontin, and J. Wakeley, 2010. Measuring the sensitivity of single-locus “neutrality tests” using a direct perturbation approach. Mol. Biol. Evol. 27:73-89. (pdf)

RoyChoudhury, A. and J. Wakeley, 2010. Sufficiency of the number of segregating sites in the limit under finite-sites mutation. Theoret. Pop. Biol. 78:118-122. (pdf)

Wakeley, J. and O. Sargsyan, 2009. Extensions of the coalescent effective population size. Genetics 181:341-345. (pdf)

Wakeley, J. and O. Sargsyan, 2009. The conditional ancestral selection graph with strong balancing selection. Theoret. Pop. Biol. 75:355-364. (pdf)

Antal, T., H. Ohtsuki, J. Wakeley, P. D. Taylor and M. Nowak, 2009. Evolution of cooperation by phenotypic similarity. Proc. Natl. Acad. Sci., USA 106:8597-8600. (pdf)

Eldon, B. and J. Wakeley, 2009. Coalescence times and FST under a skewed offspring distribution among individuals in a population. Genetics 181:615-629. (pdf)

Muirhead, C. and J. Wakeley, 2009. Modeling multiallelic selection using a Moran model. Genetics 182:1141-1157. (pdf)

Shpak, M., J. Wakeley, D. Garrigan, and R. C. Lewontin 2009. A structured coalescent process for seasonally fluctuating populations. Evolution 64:1395-1409. (pdf)

Wakeley, J. 2008. Coalescent Theory: An Introduction. Roberts & Company Publishers, Greenwood Village, Colorado.

Wakeley, J. 2008a. Complex speciation of humans and chimpanzees. Nature 452:e3-e4. (pdf)

Wakeley, J. 2008b. Conditional gene genealogies under strong purifying selection. Mol. Biol. Evol. 25:2615-2626. (pdf)

Eldon, B. and J. Wakeley, 2008. Linkage disquilibrium under skewed offspring distribution among individuals in a population. Genetics 178:1517-1532. (pdf)

Jones, D. and J. Wakeley 2008a. Recombination, gene conversion, and identity by descent at three loci. Theoret. Pop. Biol. 73:264-276. (pdf)

Jones, D. and J. Wakeley 2008b. The influence of gene conversion on linkage disequilibrium around a selective sweep. Genetics 180:1251-1259. (pdf)

Ramachandran, O., N. A. Rosenberg, M. W. Feldman and J. Wakeley, 2008. Population differentiation and migration: Coalescence times in a two-sex island model for autosomal and X-linked loci . Theoret. Pop. Biol. 74:104-114. (pdf)

Sargsyan, O. and J. Wakeley, 2008. A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms. Theoret. Pop. Biol. 74:104-114. (pdf)

Wakeley, J. and S. Lessard, 2006. Corridors for migration between large subdivided populations, and the structured coalescent. Theoret. Pop. Biol. 70:412-420. (pdf)

Watson, R. A., Weinreich, D. and J. Wakeley, 2006. Effects of intra-gene fitness interactions on the benefit of sexual recombination. Biochemical Society Transactions 3(4) (pdf preprint)

Jesus, F. F., J. Wilkins, and J. Wakeley, 2006. Expected coalescence times and segregating sites in a model of glacial cycles. Genetics and Molecular Research 5:466-474. (pdf)

Eldon, B. and J. Wakeley, 2006. Coalescent processes when the distribution of offspring number among individuals is highly skewed. Genetics 172:2621-2633. (pdf)

Matsen, F. A. and J. Wakeley, 2006. Convergence to the island-model coalescent process in populations with restricted migration. Genetics 172:701-708. (pdf)

Wakeley, J. 2005. The limits of theoretical population genetics. Genetics 169:1-7. (pdf)

Slade, P. and J. Wakeley, 2005. The ancestral selection graph and the many-demes limit. Genetics 169:1117-1131. (pdf)

Watson, R. A. and J. Wakeley, 2006. Multidimensional Epistasis and the Advantage of Sex. Proceedings of the 2005 Congress on Evolutionary Computation (CEC 2005) (pdf preprint)

Wakeley, J. 2004. Metapopulation models for historical inference. Mol. Ecol. 13:865-875. (pdf)

Wakeley, J. 2004. Recent trends in population genetics: more data! more math! simple models? J. Hered. 95:397-405. (pdf)

Wakeley, J. 2004. Metapopulations and coalescent theory. Pp. 175-198 in Ecology, Genetics, and Evolution of Metapopulations. (Ilkka Hanski and Oscar Gaggiotti, eds.) Elsevier, Oxford.

Wakeley, J. and T. Takahashi, 2004. The many-demes limit for selection and drift in a subdivided population. Theoret. Pop. Biol. 66:83-91. (pdf)

Achaz, G., S. Palmer, M. Kearny, F. Maldarelli, J. W. Mellors, J. M. Coffin and J. Wakeley, 2004. A robust measure of HIV-1 population turnover within chronically infected individuals. Mol. Biol. Evol. 21:1902-1912. (pdf)

Lessard, S. and J. Wakeley, 2004. The two-locus ancestral graph in a subdivided population: convergence as the number of demes grows in the island model. J. Math. Biol. 48:275-292. (pdf)

Wakeley, J. 2003. Polymorphism and divergence for island-model species. Genetics 163:411-420. (pdf)

Wakeley, J. 2003. Inferences about the structure and history of populations: coalescents and intraspecific phylogeography. Pp. 193-215 in The Evolution of Population Biology (Rama Singh and Marcy Uyenoyama, eds.), Cambridge University Press, Cambridge. (pdf)

Wakeley, J. and S. Lessard 2003. Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humans. Genetics 164:1043-1053. (pdf)

Wakeley, J. and T. Takahashi 2003. Gene genealogies when the sample size exceeds the effective size of the population. Mol. Biol. Evol. 20:208-213. (pdf)

Cherry, J. and J. Wakeley 2003. A diffusion approximation for selection and drift in a subdivided population. Genetics 163:421-428. (pdf)

Rouzine, I., J. Wakeley, J. M. Coffin 2003. The solitary wave of asexual evolution. Proc. Natl. Acad. Sci., USA 100:587-592. (pdf)

Arbogast, B, S. V. Edwards, J. Wakeley, P. Beerli and J. B. Slowinski 2002. Estimating divergence time from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33:707-740. (pdf)

Wilkins, J. F. and J. Wakeley 2002. The coalescent in a continuous, finite, linear population. Genetics 161:873-888. (pdf)

Wakeley, J., R. Nielsen, S. N. Liu-Cordero and K. Ardlie 2001. The discovery of single-nucleotide polymorphisms--and inferences about human demographic history. Am. J. Hum. Genet. 69:1332-1347. (pdf)

Bustamante C. D., J. Wakeley, S. Sawyer and D. L. Hartl 2001. Directional selection and the site-frequency spectrum. Genetics 159:1779-1788. (pdf)

Wakeley, J. and N. Aliacar 2001. Gene genealogies in a metapopulation. Genetics 159:893-905. (See erratum to figure 2, Genetics 160:1263-1264). (pdf)

Nielsen, R. and J. Wakeley 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896. (pdf)

Wakeley, J. 2001. The coalescent in an island model with variation among demes. Theoret. Pop. Biol. 59:133-144. (pdf)

Wakeley, J. 2000. The effects of subdivision on the genetic divergence of populations and species. Evolution 54:1092-1101. (pdf)

Kliman, R., P. Andolfatto, J. A. Coyne, F. DePaulis, M. Kreitman, A. J. Berry, J. McCarter, J. Wakeley J. Hey 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931. (pdf)

Wakeley, J. 1999. Non-equilibrium migration in human history. Genetics 153:1836-1871. (pdf)

Cummings, M. P., S. P. Otto and J. Wakeley 1999. Genes and other samples of DNA sequence data for phylogenetic inference. Biol. Bull. 196:345-350.

Wakeley, J. 1998. Segregating sites in Wright's island model. Theoret. Pop. Biol. 53:166-174. (pdf)

Wakeley, J., and J. Hey 1998. Testing speciation models with DNA sequence data. Pp. 157-175 in Molecular Approaches to Ecology and Evolution (B. Schierwater and R. DeSalle, eds.) Birkhauser-Verlag, Basel.

Wang, R. L., J. Wakeley and J. Hey 1997. Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives. Genetics 147:1091-1106.

Hey, J. and J. Wakeley 1997. A coalescent estimator of the population recombination rate. Genetics 145:833-846. (pdf)

Wakeley, J. and J. Hey 1997. Estimating ancestral population parameters. Genetics 145:847-855. (pdf)

Wakeley, J. 1997. Using the variance of pairwise differences to estimate the recombination rate. Genet. Res., Camb. 69:45-48. (pdf)

Wakeley, J. 1996. Pairwise differences under a general model of population subdivision. J. Genet. 75:81-89. (pdf)

Wakeley, J. 1996. The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. Trends in Ecology and Evolution 11:158-163. (pdf)

Wakeley, J. 1996. Distinguishing migration from isolation using the variance of pairwise differences. Theoret. Pop. Biol. 49:369-386. (pdf)

Wakeley, J. 1996. The variance of pairwise nucleotide differences in two populations with migration. Theoret. Pop. Biol. 49:39-57. (pdf)

Otto, S. P., M. P. Cummings, and J. Wakeley 1996. Inferring phylogenies from DNA sequence data: the effects of sampling. Pp. 103-115 in New Uses for New Phylogenies (P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee, eds.) Oxford University Press, New York.

Cummings, M. P., S. P. Otto and J. Wakeley 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822. (pdf)

Wakeley, J. 1994. Substitution-rate variation among sites and the estimation of transition bias. Mol. Biol. Evol. 11:436-442. (pdf)

Wakeley, J. 1993. Substitution rate variation among sites in hypervariable region I of human mitochondrial DNA. J. Mol. Evol. 37:613-623. (pdf)

If you like Mark Rothko paintings, this is an untitled one from 1963. 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.