Natural Population Analysis

lab members indicated

Pfeifer, S.P.(*), S. Laurent(*), V.C. Sousa(*), C.R. Linnen(*), M. Foll, L. Excoffier(#), H.E. Hoekstra(#), and J.D. Jensen(#). The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow. In revision, PLoS Geneticsbiorxiv

Crawford, N., D. Kelley, M. Hansen, M. Beltrame, S. Fan, S. Bowman, E. Jewett, A. Ranciaro, S. Thompson, Y. Lo, S.P. PfeiferJ.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, and S. Tishkoff. 2017. Loci associated with skin pigmentation identified in African populations. In press, Science.

Pfeifer, S.P., and J.D. Jensen. 2016. The impact of linked selection in chimpanzees: a comparative studyGBE 8: 3202-8. pdf

Kapopoulou, A., L. Mathew, A. Wong, D. Trono, and 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(#), and E.B. Rosenblum(#), 2016. The population genomics of rapid adaptation: disentangling signatures of selection and demography in White Sands lizardsMol Ecol 25(1): 306-23. pdf

Montano, V., X. Didelot, M. Foll, B. Linz, Y. Moodley(#), and J.D. Jensen(#), 2015. Worldwide population structure, long term demography, and local adaptation of Helicobacter pyloriGenetics 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, and E. Willerslev, 2014. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudo of BrazilCurr Biol 24(21): R1035-7. pdf

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

Simkin, A., J. Bailey, B. Theurkauf, F.-B. Gao, and J.D. Jensen, 2014. Inferring the evolutionary history of primate miRNA binding sites: overcoming motif counting biasesMBE 31: 1894-1901. pdf

Simkin, A., A. Wong, Y.-P. Poh, B. Theurkauf, and 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, and H.E. Hoekstra, 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339: 1312-1316pdf

Singh, N.D., J.D. Jensen, A. G. Clark, and C.F. Aquadro, 2013. Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 193(1): 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, and 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(#), and S. Akbarian(#), 2012. Human-specific histone methylation signatures at transcription start sites in prefrontal neuronsPLOS Biology. 10(11): e1001427. pdf

Domingues, V., Y.-P. Poh, B. Peterson, P. Pennings, J.D. Jensen, and H.E. Hoekstra, 2012. Targeted resequencing reveals a single recent origin of a beneficial pigment allele in cryptic beach mice. Evolution 66: 3209-23. pdf

Crisci, J., and J.D. Jensen, 2012. Evolution of the human genome: adaptive changeseLS, John Wiley & Sons, Ltdpdf

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, and 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, and J.D. Jensen, 2011. On characterizing adaptive events unique to modern humansGBE 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, and 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, and S. Paabo, 2010. A draft sequence of the Neandertal genomeScience 328: 710-722. pdf

Jensen, J.D. and D. Bachtrog, 2010. Characterizing recurrent positive selection at fast evolving genes in Drosophila mirandaGBE 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, and J. Wang, 2009. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science, 326 (5951): 433-6. pdf

Linnen, C.R., E. P. Kingsley, J.D. Jensen, and H.E. Hoekstra, 2009. On the origin and spread of an adaptive allele in Peromyscus miceScience 325 (5944): 1095-1098. pdf

Bachtrog, D., J.D. Jensen, and Z. Zhang, 2009. Pervasive adaptive evolution on a newly formed X chromosome. PLOS Biology 7(4): e1000082. 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

Singh, N.D., J.M. Macpherson, J.D. Jensen, and D.A. Petrov, 2007. X-linked and autosomal nucleotide variation in African and non-African populations of Drosophila melanogasterBMC Evol Biol 7: 202-210. pdf

Jensen, J.D., V. Bauer DuMont, A.B. Ashmore, A. Gutierrez and C.F. Aquadro, 2007. Patterns of variability and divergence at the diminutive gene region of Drosophila melanogasterGenetics 177: 832-840pdf

Casa, A.M., S.E. Mitchell, J.D. Jensen, M.T. Hamblin, A.H. Paterson, C.F. Aquadro, and S. Kresovich, 2006. Evidence for a selective sweep on chromosome 1 of cultivated sorghum. Crop Sci 46: S15-S26. pdf