J Wakeley

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescent
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 190:1433-45. 2012
  2. pmc The limits of theoretical population genetics
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 169:1-7. 2005
  3. pmc Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humans
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 164:1043-53. 2003
  4. pmc Extensions of the coalescent effective population size
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 181:341-5. 2009
  5. ncbi request reprint The many-demes limit for selection and drift in a subdivided population
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Theor Popul Biol 66:83-91. 2004
  6. ncbi request reprint Recent trends in population genetics: more data! More math! Simple models?
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 2102 Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA
    J Hered 95:397-405. 2004
  7. doi request reprint The conditional ancestral selection graph with strong balancing selection
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Theor Popul Biol 75:355-64. 2009
  8. ncbi request reprint Corridors for migration between large subdivided populations, and the structured coalescent
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 2102 Biological Laboratories, Cambridge, MA 02138, USA
    Theor Popul Biol 70:412-20. 2006
  9. doi request reprint Complex speciation of humans and chimpanzees
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nature 452:E3-4; discussion E4. 2008
  10. doi request reprint Conditional gene genealogies under strong purifying selection
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 25:2615-26. 2008

Detail Information

Publications38

  1. pmc Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescent
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 190:1433-45. 2012
    ..Differences are apparent in recent past, within ≈ <log(2)(N) generations, but then disappear as genetic lineages are traced into the more distant past...
  2. pmc The limits of theoretical population genetics
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 169:1-7. 2005
  3. pmc Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humans
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 164:1043-53. 2003
    ....
  4. pmc Extensions of the coalescent effective population size
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 181:341-5. 2009
    ..Third, even if the coalescent effective population size does not exist in the mathematical sense, it may be difficult to reject Kingman's coalescent using genetic data...
  5. ncbi request reprint The many-demes limit for selection and drift in a subdivided population
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Theor Popul Biol 66:83-91. 2004
    ..Selection is assumed to be weak, in inverse proportion to the number of demes, and the results hold for any deme sizes and migration rates greater than zero. The distribution of allele frequencies among demes is also described...
  6. ncbi request reprint Recent trends in population genetics: more data! More math! Simple models?
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 2102 Biological Laboratories, 16 Divinity Ave, Cambridge, MA 02138, USA
    J Hered 95:397-405. 2004
    ....
  7. doi request reprint The conditional ancestral selection graph with strong balancing selection
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Theor Popul Biol 75:355-64. 2009
    ..We also present a more rigorous demonstration that the neutral conditional ancestral process converges to the Kingman coalescent in the limit as the mutation rate tends to infinity...
  8. ncbi request reprint Corridors for migration between large subdivided populations, and the structured coalescent
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 2102 Biological Laboratories, Cambridge, MA 02138, USA
    Theor Popul Biol 70:412-20. 2006
    ..This justifies the application of a modified structured coalescent to some hierarchically structured populations...
  9. doi request reprint Complex speciation of humans and chimpanzees
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nature 452:E3-4; discussion E4. 2008
    ..2, for example). I therefore believe that their claim of hybridization is unwarranted...
  10. doi request reprint Conditional gene genealogies under strong purifying selection
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 25:2615-26. 2008
    ..These results extend the idea of a soft selective sweep to deleterious alleles and have implications for the interpretation of polymorphism among disease-causing alleles in humans...
  11. ncbi request reprint Gene genealogies when the sample size exceeds the effective size of the population
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
    Mol Biol Evol 20:208-13. 2003
    ....
  12. pmc Polymorphism and divergence for island-model species
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 163:411-20. 2003
    ..Estimates of the strength of selection are much less strongly affected and always in a conservative direction...
  13. pmc Gene genealogies in a metapopulation
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 159:893-905. 2001
    ..Extinction and recolonization, in contrast, can produce a mode in the site-frequency distribution at intermediate frequencies, even in a sample from a single deme...
  14. pmc The discovery of single-nucleotide polymorphisms--and inferences about human demographic history
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Am J Hum Genet 69:1332-47. 2001
    ..An important conclusion of this work is that, in demographic or other studies, SNP data are useful only to the extent that their ascertainment can be modeled...
  15. ncbi request reprint The effects of subdivision on the genetic divergence of populations and species
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Evolution 54:1092-101. 2000
    ..It can also have a profound effect on the estimation of divergence times...
  16. pmc Distinguishing migration from isolation: a Markov chain Monte Carlo approach
    R Nielsen
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Genetics 158:885-96. 2001
    ..The use of the method is illustrated in an application to mitochondrial DNA sequence data from a fish species: the threespine stickleback (Gasterosteus aculeatus)...
  17. pmc Coalescent processes when the distribution of offspring number among individuals is highly skewed
    Bjarki Eldon
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 172:2621-33. 2006
    ..The data suggest the presence of rare reproduction events in which approximately 8% of the population is replaced by the offspring of a single individual...
  18. ncbi request reprint A robust measure of HIV-1 population turnover within chronically infected individuals
    G Achaz
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 21:1902-12. 2004
    ..The definition and interpretation of estimates of such "effective" population parameters are discussed...
  19. pmc The coalescent in a continuous, finite, linear population
    Jon F Wilkins
    Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 161:873-88. 2002
    ..The pattern of pairwise nucleotide differences predicted by the model is compared to data collected from sardine populations. The sardine data are used to illustrate how demographic parameters can be estimated using the model...
  20. pmc Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci
    Sohini Ramachandran
    Society of Fellows, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Theor Popul Biol 74:291-301. 2008
    ..We apply our results to microsatellite data from the Human Genome Diversity Panel, and we examine the male and female migration rates implied by observed F(ST) values...
  21. pmc Modeling multiallelic selection using a Moran model
    Christina A Muirhead
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Room 4100, Cambridge, Massachusetts 02138, USA
    Genetics 182:1141-57. 2009
    ..Our results can be applied to any model of multiallelic selection in which fitness is solely a function of allele frequency...
  22. pmc The influence of gene conversion on linkage disequilibrium around a selective sweep
    Danielle A Jones
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 180:1251-9. 2008
    ..We show that one of the conclusions is strongly affected by gene conversion: when gene conversion is present, there may be substantial LD between two loci on opposite sides of a selective sweep...
  23. doi request reprint A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms
    Ori Sargsyan
    Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Theor Popul Biol 74:104-14. 2008
    ..Our work suggests that the power to detect a "sweepstakes effect" in a sample of DNA sequences from marine organisms depends on the sample size...
  24. pmc Linkage disequilibrium under skewed offspring distribution among individuals in a population
    Bjarki Eldon
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 178:1517-32. 2008
    ..Simulations support the analytical results but show that the variance of linkage disequilibrium is very large...
  25. doi request reprint Recombination, gene conversion, and identity-by-descent at three loci
    Danielle Jones
    Department of Organismic and Evolutionary Biology, Harvard University, 4092 4100 Biological Laboratories, 16 Divinity Avenue, Cambridge, MA, 02138, USA
    Theor Popul Biol 73:264-76. 2008
    ..This implies that measures of genetic identity in larger samples will be needed to distinguish between gene conversion and recombination...
  26. ncbi request reprint Metapopulation models for historical inference
    John Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Ecol 13:865-75. 2004
    ..Examples illustrate when the usual diffusion limit is appropriate and when it is not. Some shortcomings and extensions of the model are considered, and the relevance of such models to understanding human history is discussed...
  27. pmc Convergence to the island-model coalescent process in populations with restricted migration
    Frederick A Matsen
    Program for Evolutionary Dynamics and the Department of Mathematics, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 172:701-8. 2006
    ..We investigate the rate of convergence to this limit using simulations...
  28. pmc Coalescence times and FST under a skewed offspring distribution among individuals in a population
    Bjarki Eldon
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 181:615-29. 2009
    ..The results can explain the observed genetic heterogeneity among subpopulations of certain marine organisms despite substantial gene flow...
  29. pmc A diffusion approximation for selection and drift in a subdivided population
    Joshua L Cherry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 163:421-8. 2003
    ..This explains how the fixation probability of a selected allele can be unaffected by population subdivision despite the fact that subdivision increases N(e), for the product N(e)s(e) is not altered by subdivision...
  30. ncbi request reprint The coalescent in an island model of population subdivision with variation among demes
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Theor Popul Biol 59:133-44. 2001
    ....
  31. pmc Measuring the sensitivity of single-locus "neutrality tests" using a direct perturbation approach
    Daniel Garrigan
    Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA
    Mol Biol Evol 27:73-89. 2010
    ..The utility of using empirical, genomic distributions of test statistics, instead of the theoretical steady-state distribution, is discussed as an alternative for improving the statistical inference of natural selection...
  32. pmc Nonequilibrium migration in human history
    J Wakeley
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 153:1863-71. 1999
    ..This is consistent with a change in the rates of migration among human subpopulations from ancient low levels to present high ones...
  33. pmc Directional selection and the site-frequency spectrum
    C D Bustamante
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 159:1779-88. 2001
    ..We also find that the LRT is not robust to deviations from the assumption of independence among sites...
  34. pmc Evolution of cooperation by phenotypic similarity
    Tibor Antal
    Program for Evolutionary Dynamics and Department of Mathematics, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 106:8597-600. 2009
    ..We also derive the fundamental condition for any two-strategy symmetric game and consider high-dimensional phenotype spaces...
  35. pmc Extending coalescent theory to autotetraploids
    B Arnold
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 192:195-204. 2012
    ..We also consider the possibility of double reduction, a phenomenon unique to polysomic inheritance, and show that its effects on gene genealogies are similar to partial self-fertilization...
  36. pmc The structured ancestral selection graph and the many-demes limit
    Paul F Slade
    School of Mathematics and Statistics, SUBIT, University of Sydney, New South Wales 2006, Australia
    Genetics 169:1117-31. 2005
    ..We find that a similar effect also increases the sensitivity of the genealogy to selection...
  37. ncbi request reprint The two-locus ancestral graph in a subdivided population: convergence as the number of demes grows in the island model
    Sabin Lessard
    Departement de Mathematiques et de Statistique, Universite de Montreal, Canada
    J Math Biol 48:275-92. 2004
    ..Simulations imply that convergence to a rescaled panmictic ancestral recombination graph occurs for any number of sites as the number of demes approaches infinity...
  38. pmc The solitary wave of asexual evolution
    Igor M Rouzine
    Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111, USA
    Proc Natl Acad Sci U S A 100:587-92. 2003
    ..The model explains a logarithmic dependence of steady-state fitness on the population size reported recently for an RNA virus...