PopGen Theory & Methodology

lab members indicated

Soni, V., and J.D. Jensen. 2024. Temporal challenges in detecting balancing selection from population genomic data. G3 14: jkae069. pdf

Soni, V., S.P. Pfeifer, and J.D. Jensen. 2024. The effect of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects. GBE 16: evae004. pdf

Charlesworth, B., and J.D. Jensen. 2024. Population genetics. Encyclopedia of Biodiversity, 3rd edition. Vol. 7: 467-483.

Soni, V., P. Johri, and J.D. Jensen. 2023. Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models. Evolution 77: 2113-2127. pdf

Freund, F., E. Kerdoncuff, S. Matuszewski, M. Lapierre, M. Hildebrandt, J.D. Jensen, L. Ferretti, A. Lambert, T. Sackton, and G. Achaz. 2023. Interpreting the pervasive observation of U-shaped site frequency spectra. PLOS Genetics 19: e1010677. pdf

Ghafoor, S., J. Santos, C.J. Versoza, J.D. Jensen, and S.P. Pfeifer. 2023. The impact of sample size and population history on observed mutational spectra: a case study in human and chimpanzee populations. GBE 15: evad019. pdf

Charlesworth, B., and J.D. Jensen. 2023. Population genetic considerations regarding evidence for biased mutation rates in Arabidopsis thaliana. MBE 40: msac275. pdf

Jensen, J.D. 2023. Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes. Heredity 130: 109-110. pdf

Charlesworth, B., and J.D. Jensen. 2022. Some complexities in interpreting apparent effects of hitchhiking: a commentary on Gompert et al. 2022. Mol Ecol 31: 4440-4443. pdf

Charlesworth, B., and J.D. Jensen. 2022. How can we resolve Lewontin’s Paradox? GBE 14(7): evac096. pdf

Johri, P., A. Eyre-Walker, R.N. Gutenkunst, K.E. Lohmueller, and J.D. Jensen. 2022. On the prospect of achieving accurate joint estimation of selection with population historyGBE 14(7): evac088. pdf

Johri, P., C.F. Aquadro, M. Beaumont, B. Charlesworth, L. Excoffier, A. Eyre-Walker, P.D. Keightley, M. Lynch, G. McVean, B.A. Payseur, S.P. Pfeifer, W. Stephan, and J.D. Jensen. 2022. Recommendations for improving statistical inference in population genomics. PLOS Biology 20(5): e3001669. pdf

Johri, P., W. Stephan, and J.D. Jensen. 2022. Soft selective sweeps: addressing new definitions, evaluating competing models, and interpreting empirical outliers. PLOS Genetics 18(2): e1010022. pdf

Johri, P.(*), B. Charlesworth(*), E.K. Howell, M. Lynch(#), and J.D. Jensen(#). 2021. Revisiting the notion of deleterious sweeps. Genetics 219: iyab094. pdf

Charlesworth, B., and J.D. Jensen. 2021. Effects of selection at linked sites on patterns of genetic variability. AREES 52: 177-197. pdf

Johri, P., K. Riall, H. Becher, L. Excoffier, B. Charlesworth, and J.D. Jensen. 2021. The impact of purifying and background selection on the inference of population history: problems and prospects. MBE 38: 2986-3003. pdf

Harris, R.B., and J.D. Jensen. 2020. Considering genomic scans for selection as coalescent model choice. GBE 12: 871-77. pdf

Johri, P., B. Charlesworth, and J.D. Jensen. 2020. Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection. Genetics 215: 173-92. pdf

Sackman, A., R.B. Harris, and J.D. Jensen. 2019. Inferring demography and selection in organisms characterized by skewed offspring distributions. Genetics 211: 1019-28. pdf

Jensen, J.D., B.A. Payseur, W. Stephan, C.F. Aquadro, M. Lynch, D. Charlesworth, and B. Charlesworth. 2019. The importance of the Neutral Theory in 1968 and 50 years on: a response to Kern & Hahn 2018. Evolution 73: 111-14. pdf

Harris, R.B.(*), A. Sackman(*), and J.D. Jensen. 2018. On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses. PLOS Genetics 14(12): e1007859. pdf

Matuszewski, S., M.E. Hildebrandt, G. Achaz, and J.D. Jensen. 2018. Coalescent processes with skewed offspring distributions and non-equilibrium demography. Genetics 208: 323-38. pdf

Matuszewski, S., L. OrmondC. Bank, and J.D. Jensen. 2017. Two sides of the same coin: a population genetics perspective on lethal mutagenesis and mutational meltdownVirus Evol 3: 1-5pdf

Irwin, K.K., S. LaurentS. MatuszewskiS. VuilleumierL. OrmondH. ShimC. Bank, and J.D. Jensen. 2016. On the importance of skewed offspring distributions and background selection in viral population genetics. Heredity 117: 393-99. pdf

Matuszewski, S.(*), M.E. Hildebrandt(*), A.-H. Ghenu, J.D. Jensen, and C. Bank. 2016. A statistical guide to the design of deep mutational scanning experimentsGenetics 204: 77-87. pdf

Ferrer-Admetlla, A., C. Leuenberger, J.D. Jensen, and D. Wegmann. 2016. An approximate Markov model for the Wright-Fisher diffusion and its application to time series dataGenetics 203: 831-46. pdf

Shim, H., S. LaurentS. MatuszewskiM. Foll, and J.D. Jensen. 2016. Detecting and quantifying changing selection intensities from time-sampled polymorphism dataG3 6: 893-904pdf

Alcala, N., J.D. Jensen, A. Telenti, and S. Vuilleumier. 2016. The genomic signature of population reconnection following isolation: from theory to HIV. G3 6: 107-20pdf

Jensen, J.D.M. Foll, and L. Bernatchez. 2016. Introduction: the past, present, and future of genomic scans for selectionMol Ecol 25: 1-4. pdf

Ormond, L., M. FollG. EwingS. Pfeifer, and J.D. Jensen, 2016. Inferring the age of a fixed beneficial alleleMol Ecol 25: 157-9. pdf

Ewing, G. and J.D. Jensen, 2016. The consequences of not accounting for background selection in demographic inferenceMol Ecol 25: 135-141. pdf

Mathew, L. and J.D. Jensen, 2015. Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demographyFront Genet. 6: 268. pdf

Mahajan, S.J. Crisci, A. Wong, S. Akbarian, M. Foll(#), and J.D. Jensen(#), 2015. Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection. Front Genet. 6: 190. pdf

Ewing, G., P. Reiff, and J.D. Jensen, 2015. PopPlanner: Visually constructing demographic models for simulationFront Genet. 6: 150. pdf

Foll, M.(*)H. Shim(*), and J.D. Jensen, 2015. A Wright-Fisher ABC-based approach for inferring per-site effective population sizes and selection coefficients from time-sampled dataMol Ecol Res 15: 87-98. pdf

Bank, C.M. FollA. Ferrer-AdmetllaG. Ewing, and J.D. Jensen, 2014. Thinking too positive? Revisiting current methods in population genetic selection inferenceTrends Genet 30: 540-6. pdf

Poh, Y.-P., V. Domingues, H.E. Hoekstra, and J.D. Jensen, 2014. On the prospect of identifying adaptive loci in recently bottlenecked populationsPLOS One 9(11): e110579. pdf

Jensen, J.D., 2014. On the unfounded enthusiasm for soft selective sweepsNat Comm 5: 5281. pdf

Bank, C., R.T. Hietpas, A. Wong, D.N.A. Bolon(#), and J.D. Jensen(#), 2014. A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environmentsGenetics 196: 841-52. pdf

Foll, M.(*)Y.-P. Poh(*)N. RenzetteA. Ferrer-AdmetllaH. Shim, A.-S. Malaspinas, G. EwingC. Bank, P. Liu, D. Wegmann, D. R. Caffrey, K.B. Zeldovich, D.N.A. Bolon, J. Wang, T.F. Kowalik, C.A. Schiffer, R.W. Finberg, and J.D. Jensen, 2014. Influenza virus drug resistance: a time-sampled population genetics perspective. PLOS Genetics 10(2): e1004185. pdf

Ewing, G., and J.D. Jensen, 2014. Distinguishing neutral from deleterious mutations in growing populationsFront Genet. 5: 7. pdf

Crisci, J., Y.-P. PohS. Mahajan, and J.D. Jensen, 2013. The impact of equilibrium assumptions on tests of selection. Front Genet. 4: 235. pdf

Joost, S., S. Vuilleumier, J.D. Jensen, S. Schoville, K. Leempoel, S. Stucki, C. Melo de Lima, J. Rolland, I. Widmer, and S. Manel, 2013. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population geneticsMol Ecol 22: 3659-3665. pdf

Pavlidis, P., J.D. Jensen, W. Stephan, A. Stamatakis, 2012. A critical assessment of story-telling: GO categories and the importance of validating genomic scans. MBE 29: 3237-48. pdf

Crisci, J., Y.-P. PohA. BeanA. Simkin, and J.D. Jensen, 2012. Recent progress in polymorphism-based population genetic inferenceJ Hered 103: 287-96. pdf

Sinha, P., A. Dincer, D. Virgil, G. Xu, Y.-P. Poh, and J.D. Jensen, 2011. On detecting selective sweeps using single genomesFront Genet. 2: 85-90. pdf

Crisci, J., A. Wong, J. Good, and J.D. Jensen, 2011. On characterizing adaptive events unique to modern humansGBE 3: 791-798. pdf

Jensen, J.D. and D. Bachtrog, 2011. Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin Domain. GBE 3: 687-701. pdf

Cutler, D.J. and J.D. Jensen, 2010. To pool, or not to pool. Genetics 186: 41-3. pdf

Pavlidis, P., J.D. Jensen, and W. Stephan, 2010. Searching for footprints of positive selection in whole-genome SNP data from non-equilibrium populations. Genetics 185: 907-22. pdf

Jensen, J.D., and O.J. Rando, 2010. Recent evidence for pervasive adaptation targeting gene expression attributable to population size change. PNAS 107: E109-110. pdf

Pool, J. E., I. Hellmann, J.D. Jensen, and R. Nielsen. 2010, Population genetic inference from genomic sequence variationGenome Res 20: 291-300. pdf

Jensen, J.D., 2009. On reconciling single and recurrent hitchhiking modelsGBE 1: 320-4. pdf

Jensen, J.D., K.R. Thornton, and P. Andolfatto, 2008. An approximate Bayesian estimator suggests strong recurrent selective sweeps in Drosophila. PLOS Genetics 4(9): e1000198. pdf

Jensen, J.D., K.R. Thornton, and C.F. Aquadro, 2008. Inferring selection in partially sequenced regionsMBE 25: 438-46. pdf

Jensen, J.D., K.R. Thornton, C.D. Bustamante, and C.F. Aquadro, 2007. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics 176: 2371-2379pdf

Jensen, J.D., A. Wong, and C.F. Aquadro, 2007. Approaches for identifying targets of positive selectionTrends Genet 23: 484-491. pdf

Thornton, K.R. and J.D. Jensen, 2007. Controlling the false positive rate in multi-locus genome scans for selection. Genetics 175: 737-750. pdf

Thornton, K.R., J.D. Jensen, C. Bequet and P. Andolfatto, 2007. Progress and prospects in mapping recent selection in the genomeHeredity 98: 340-8. pdf

Jensen, J.D., Y. Kim, V. Bauer DuMont, C.F. Aquadro, and C.D. Bustamante, 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410. pdf