Natural Population Analysis

lab members indicated

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(#), and C. Papageorgopoulou(#). 2021. The genomic history of the Aegean palatial civilizations. Accepted, Cell.

Jones, M.R., L.S. Mills, J.D. Jensen, and 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, and 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, and 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, and 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, and 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, and 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(#), and 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. 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. Science 358(6365). pdf

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: 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 populationsPLOS 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 melanogasterGenetics 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, and B. Deplancke, 2012. Genomic variation and its impact on gene expression in Drosophila melanogasterPLOS 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. Evidence of adaptation from ancestral variation in young populations of 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 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, and 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, and H.E. Hoekstra, 2009. On the origin and spread of an adaptive allele in deer miceScience 325: 1095-1098. pdf

Bachtrog, D., J.D. Jensen, and Z. Zhang, 2009. Accelerated 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

Wong, A.W., J.D. Jensen, J.E. Pool and 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, and D.A. Petrov, 2007. Similar levels of 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 melanogaster: a complex pattern suggests an ancestral selective sweepGenetics 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