Research Topics
| J WakeleySummaryAffiliation: Harvard University Country: USA Publications
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Publications
Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescentJohn 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...- The limits of theoretical population geneticsJohn Wakeley
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genetics 169:1-7. 2005 - Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humansJohn Wakeley
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genetics 164:1043-53. 2003.... - Extensions of the coalescent effective population sizeJohn 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... 
The many-demes limit for selection and drift in a subdivided populationJohn 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...- 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.... 
The conditional ancestral selection graph with strong balancing selectionJohn 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...- Corridors for migration between large subdivided populations, and the structured coalescentJohn 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... - Complex speciation of humans and chimpanzeesJohn 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... - Conditional gene genealogies under strong purifying selectionJohn 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... - Gene genealogies when the sample size exceeds the effective size of the populationJohn Wakeley
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
Mol Biol Evol 20:208-13. 2003.... - Polymorphism and divergence for island-model speciesJohn 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... - Gene genealogies in a metapopulationJ 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... - The discovery of single-nucleotide polymorphisms--and inferences about human demographic historyJ 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... - The effects of subdivision on the genetic divergence of populations and speciesJ 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... - Distinguishing migration from isolation: a Markov chain Monte Carlo approachR 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)... - Coalescent processes when the distribution of offspring number among individuals is highly skewedBjarki 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... - A robust measure of HIV-1 population turnover within chronically infected individualsG 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... - The coalescent in a continuous, finite, linear populationJon 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... - Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked lociSohini 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... - Modeling multiallelic selection using a Moran modelChristina 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... - The influence of gene conversion on linkage disequilibrium around a selective sweepDanielle 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... - A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organismsOri 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... - Linkage disequilibrium under skewed offspring distribution among individuals in a populationBjarki 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... - Recombination, gene conversion, and identity-by-descent at three lociDanielle 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... - Metapopulation models for historical inferenceJohn 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... - Convergence to the island-model coalescent process in populations with restricted migrationFrederick 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... - Coalescence times and FST under a skewed offspring distribution among individuals in a populationBjarki 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... - A diffusion approximation for selection and drift in a subdivided populationJoshua 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... - The coalescent in an island model of population subdivision with variation among demesJ Wakeley
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Theor Popul Biol 59:133-44. 2001.... - Measuring the sensitivity of single-locus "neutrality tests" using a direct perturbation approachDaniel 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... - Nonequilibrium migration in human historyJ 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... - Directional selection and the site-frequency spectrumC 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... - Evolution of cooperation by phenotypic similarityTibor 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... - Extending coalescent theory to autotetraploidsB 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... - The structured ancestral selection graph and the many-demes limitPaul 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... - The two-locus ancestral graph in a subdivided population: convergence as the number of demes grows in the island modelSabin 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... - The solitary wave of asexual evolutionIgor 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...