lab members indicated; # co-corresponding authors; * joint first-authors
Soni, V., C. Versoza, E.J. Vallender, J.D. Jensen#, S.P. Pfeifer#. Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (Callithrix jacchus) from high-quality, whole-genome, population-level data. in revision.
Terbot, J., V. Soni, C. Versoza, M. Milhaven, A. Calahorra-Oliart, D. Shah, S.P. Pfeifer#, J.D. Jensen#. Interpreting patterns of X chromosomal relative to autosomal diversity in aye-ayes (Daubentonia madagascariensis). in review.
Soni, V., C. Versoza, S.P. Pfeifer#, J.D. Jensen#. Estimating the distribution of fitness effects in aye-ayes (Daubentonia madagascariensis), accounting for population history as well as mutation and recombination rate heterogeneity. in review.
Soni, V.*, C. Versoza*, J. Terbot, J.D. Jensen#, S.P. Pfeifer#. Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis). in review.
Versoza, C., J.D. Jensen, S.P. Pfeifer. The landscape of structural variation in aye-ayes (Daubentonia madagascariensis). in revision.
Versoza, C.*, A. Lloret-Villas*, J.D. Jensen, S.P. Pfeifer. 2025. A pedigree-based map of crossovers and non-crossovers in aye-ayes (Daubentonia madagascariensis). GBE, in press.
Soni, V., J. Terbot, C. Versoza, S.P. Pfeifer#, J.D. Jensen#. 2025. A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model. G3, in press.
Soni, V., J.D. Jensen. 2025. Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data. G3, in press.
Versoza, C., E. Ehmke, J.D. Jensen, S.P. Pfeifer. 2025. Characterizing the rates and patterns of de novo germline mutations in the aye-aye (Daubentonia madagascariensis). MBE, in press.
Terbot, J., V. Soni, C. Versoza, S.P. Pfeifer#, J.D. Jensen#. 2025. Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data. GBE 17: evae281. pdf
Versoza, C.*, S. Weiss*, R. Johal, B. La Rosa, J.D. Jensen, S.P. Pfeifer. 2024. Novel insights into the landscape of crossover and non-crossover events in rhesus macaques (Macaca mulatta). GBE 16: evad223. pdf
Johri, P., S.P. Pfeifer, J.D. Jensen. 2023. Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history. MBE 40: msad100. pdf
Hager, E.R.*, O.S. Harringmeyer*, T.B. Wooldridge, S. Theingi, J.T. Gable, S. McFadden, B. Neugeboren, K.M. Turner, J.D. Jensen, H.E. Hoekstra. 2022. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science 377: 399-405. pdf
Clemente, F., M. Unterlander, O. Dolgova, C. Amorim, F. Coroado-Santos, S. Neuenschwander, E. Ganiatsou, D. Cruz Davalos, L. Anchieri, F. Michaud, L. Winkelbach, J. Blocher, Y. Cardenas, B. Sousa da Mota, E. Kalliga, A. Souleles, I. Kontopoulos, G. Karamitrou-Mendessidi, O. Philaniotou, A. Sampson, D. Theodorou, M. Tsipopoulou, I. Akamatis, P. Halstead, K. Kotsakis, D. Urem-Kotsou, D. Panagiotopoulos, C. Ziota, S. Triantaphyllou, O. Delaneau, J.D. Jensen, J. Morena-Mayar, J. Burger, V. Sousa, O. Lao, A.-S. Malaspinas#, C. Papageorgopoulou#. 2021. The genomic history of the Aegean palatial civilizations. Cell 184: 2565-2586. pdf
Jones, M.R., L.S. Mills, J.D. Jensen, J.M. Good. 2020. Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range. Evolution 74: 2033-45. pdf
Jones, M.R., L.S. Mills, J.D. Jensen, J.M. Good. 2020. The origin and spread of locally adaptive seasonal camouflage in snowshoe hares. Am Nat. 196: 316-32. pdf
Harris, R.B., K.K. Irwin, M.R. Jones, S. Laurent, R.D.H. Barrett, M.W. Nachman, J.M. Good, C.R. Linnen, J.D. Jensen, S.P. Pfeifer. 2020. The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity 124: 1-14. pdf
Barrett, R.D.H.*, S. Laurent*, R. Mallarino*, S.P. Pfeifer, C.C. Xu, M. Foll, K. Wakamatsu, J. Duke-Cohan, J.D. Jensen, H.E. Hoekstra. 2019. Linking a mutation to survival in wild mice. Science 363: 499-504. pdf
Kapopoulou, A., S.P. Pfeifer, J.D. Jensen, S. Laurent. 2018. The demographic history of African Drosophila melanogaster. GBE 10(9): 2338-42. pdf
Jones, M.R., L. Mills, P. Alves, C. Callahan, J. Alves, D. Lafferty, F. Jiggins, J.D. Jensen, J. Melo-Ferreira, J.M. Good. 2018. Adaptive introgression underlies polymorphic seasonal camouflage in Snowshoe Hares. Science 360: 1355-58. pdf
Pfeifer, S.P.*, S. Laurent*, V.C. Sousa*, C.R. Linnen*, M. Foll, L. Excoffier#, H.E. Hoekstra#, J.D. Jensen#. 2018. The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow. MBE 35: 792-806. pdf
Crawford, N., D. Kelley, M. Hansen, M. Beltrame, S. Fan, S. Bowman, E. Jewett, A. Ranciaro, S. Thompson, Y. Lo, S.P. Pfeifer, J.D. Jensen, M. Campbell, W. Beggs, E. Hormozdiari, S. Mpoloka, G. Mokone, T. Nyambo, D. Meskel, G. Belay, J. Haut, NISC Comparative Sequencing Program, H. Rothschild, L. Zon, Y. Zhou, M. Kovacs, M. Xu, T. Zhang, K. Bishop, J. Sinclair, C. Rivas, E. Elliot, J. Choi, S. Li, B. Hicks, S. Burgess, C. Abnet, D. Watkins-Chow, E. Oceana, Y. Song, E. Eskin, K. Brown, M. Marks, S. Loftus, W. Pavan, M. Yeager, S. Chancock, S. Tishkoff. 2017. Loci associated with skin pigmentation identified in African populations. Science 358(6365). pdf
Pfeifer, S.P., J.D. Jensen. 2016. The impact of linked selection in chimpanzees: a comparative study. GBE 8: 3202-8. pdf
Kapopoulou, A., L. Mathew, A. Wong, D. Trono, J.D. Jensen. 2016. The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution 70: 167-80. pdf
Laurent, S.*, S. Pfeifer*, M. Settles, S. Hunter, K. Hardwick, L. Ormond, V. Sousa, J.D. Jensen#, E.B. Rosenblum#. 2016. The population genomics of rapid adaptation: disentangling signatures of selection and demography in White Sands lizards. Mol Ecol 25: 306-23. pdf
Montano, V., X. Didelot, M. Foll, B. Linz, Y. Moodley#, J.D. Jensen#. 2015. Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori. Genetics 200: 947-63. pdf
Malaspinas, A.-S., O. Lao, H. Schroeder, M. Rasmussen, M. Raghavan, I. Moltke, P.F. Campos, V.F. Goncalves, S. Rasmussen, F. Santana Sagredo, A. Albrechtsen, M.E. Allentoft, P.L.F. Johnson, M. Li, S. Reis, D.V. Bernardo, A.T. Duggan, M. Bastos, E. Hodges, G.J. Hannon, M. DeGiorgio, Y. Wang, J. Stenderup, S. Brunak, T. Sicheritz-Ponten, L. Orlando, T.D. Price, J.D. Jensen, R. Nielsen, J. Heinemeier, J. Olsen, C. Rodrigues-Carvalho, M. Mirazon Lahr, W. Neves, M. Kayser, T. Higham, M. Stoneking, S.D.J. Pena, E. Willerslev. 2014. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudo of Brazil. Curr Biol 24(21): R1035-7. pdf
Poh, Y.-P., V. Domingues, H.E. Hoekstra, J.D. Jensen. 2014. On the prospect of identifying adaptive loci in recently bottlenecked populations. PLOS One 9(11): e110579. pdf
Simkin, A., J. Bailey, B. Theurkauf, F.-B. Gao, J.D. Jensen. 2014. Inferring the evolutionary history of primate miRNA binding sites: overcoming motif counting biases. MBE 31: 1894-1901. pdf
Simkin, A., A. Wong, Y.-P. Poh, B. Theurkauf, J.D. Jensen. 2013. Recurrent and recent selective sweeps in the piRNA pathway. Evolution 67: 1081-90. pdf
Linnen, C.R., Y.-P. Poh, B. Peterson, R. Barrett, J. Larson, J.D. Jensen, H.E. Hoekstra. 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339: 1312-1316. pdf
Singh, N.D., J.D. Jensen, A. G. Clark, C.F. Aquadro. 2013. Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 193: 215-28. pdf
Massouras, A., S.M. Waszak, M. Albarca, K. hens, W. Westphal, J.F. Ayroles, E.T. Dermitzakis, E.A. Stone, J.D. Jensen, T.F.C. Mackay, B. Deplancke. 2012. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLOS Genetics 8(11): e1003055. pdf
Shulha, H.*, J. Crisci*, D. Reshetov*, J.S. Tushir, I. Cheung, R. Bharadwaj, H.J. Chou, I. Houston, C.J. Peter, A.C. Mitchell, W-D. Yao, R.H. Myers, J-F. Chen, T. Preuss, E. Rogaev, J.D. Jensen#, Z. Weng#, S. Akbarian#. 2012. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLOS Biology. 10(11): e1001427. pdf
Domingues, V., Y.-P. Poh, B. Peterson, P. Pennings, J.D. Jensen, H.E. Hoekstra. 2012. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution 66: 3209-23. pdf
Crisci, J., J.D. Jensen. 2012. Evolution of the human genome: adaptive changes. eLS, John Wiley & Sons, Ltd. pdf
Xu, X.*, S. Ge*, J.D. Jensen*, R. Gutenkunst*, J. Li*, X. Li*, L. Fang, L. Huang, K. Ye, W. He, G. Zhang, X. Zheng, F. Zhang, F. Hu, Y. Li, C. Yu, Y. Guo, D. Li, K. Kristiansen, X. Zhang, J. Wang, R. Nielsen, J. Wang, W. Wang. 2011. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30: 105-11. pdf
Crisci, J., A. Wong, J. Good, J.D. Jensen. 2011. On characterizing adaptive events unique to modern humans. GBE 3: 791-798. pdf
Albert, F.W., E. Hodges, J.D. Jensen, F. Besnier, Z. Xuan, M. Rooks, A. Bhattacharjee, L. Brizuela, J.M. Good, R. E. Green, H. Burbano, I.Z. Plyusnina, L. Trut, L. Andersson, T. Schoneberg, O. Carlborg, G.J. Hannon, S. Paabo. 2011. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity 107: 205-14. pdf
Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M. H-Y. Fritz, N. Hansen, E.Y. Durand, A.-S. Malaspinas, J.D. Jensen, T. Marques-Bonet, C. Alkan, M. Meyer, K. Prufer, H.A. Burbano, J.M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Hober, B. Hoffner, M. Siegemund, A. Weihmann, C. Nusbaum, E.S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, V.B. Doronichev, L.V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R. Schmitz, P. Johnson, E.E. Eichler, D. Flash, E. Birney, J.C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich, S. Paabo. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722. pdf
Jensen, J.D., D. Bachtrog. 2010. Characterizing recurrent positive selection at fast evolving genes in Drosophila miranda and Drosophila pseudoobscura. GBE 2: 371-8. pdf
Xia, Q., Y. Guo, Z. Zheng, D. Li, Z. Xuan, Z. Li, F. Dai, Y. Li, D. Cheng, R. Li, T. Cheng, T. Jiang, C. Becquet, X. Xu, C. Liu, X. Zha, W. Fan, Y. Lin, Y. Shen, L. Jiang, J.D. Jensen, I. Hellmann, S. Tang, P. Zhao, H. Xu, C. Yu, G. Zhang, J. Li, J. Cao, S. Liu, N. He, Y. Zhou, H. Liu, J. Zhao, C. Ye, C. Du, G. Pan, A. Zhao, H. Shao, W. Zeng, P. Wu, C. Li, M. Pan, J. Li, X. Yin, D. Li, J. Wang, H. Zheng, W. Wang, X. Zhang, S. Li, H. Yang, C. Lu, R. Nielsen, Z. Zhou, J. Wang, Z. Xiang, J. Wang. 2009. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: 433-6. pdf
Linnen, C.R., E. P. Kingsley, J.D. Jensen, H.E. Hoekstra. 2009. On the origin and spread of an adaptive allele in deer mice. Science 325: 1095-1098. pdf
Bachtrog, D., J.D. Jensen, Z. Zhang. 2009. Accelerated adaptive evolution on a newly formed X chromosome. PLOS Biology 7(4): e1000082. pdf
Jensen, J.D., K.R. Thornton, P. Andolfatto. 2008. An approximate Bayesian estimator suggests strong recurrent selective sweeps in Drosophila. PLOS Genetics 4(9): e1000198. pdf
Wong, A.W., J.D. Jensen, J.E. Pool, C.F. Aquadro. 2007. Phylogenetic incongruence in the Drosophila melanogaster species group. MPE 43: 1138-50. pdf
Singh, N.D., J.M. Macpherson, J.D. Jensen, D.A. Petrov. 2007. Similar levels of X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogaster. BMC Evol Biol 7: 202-210. pdf
Jensen, J.D., V. Bauer DuMont, A.B. Ashmore, A. Gutierrez, C.F. Aquadro. 2007. Patterns of variability and divergence at the diminutive gene region of Drosophila melanogaster: a complex pattern suggests an ancestral selective sweep. Genetics 177: 832-840. pdf
Casa, A.M., S.E. Mitchell, J.D. Jensen, M.T. Hamblin, A.H. Paterson, C.F. Aquadro, S. Kresovich. 2006. Evidence for a selective sweep on chromosome 1 of cultivated sorghum. Crop Sci 46: S15-S26. pdf