Publications by lab members

Word cloud from abstracts 2015-2017

Names of lab members are underlined. Click here for software and supplementary materials.

Preprints

Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Sankararaman, S., Andolfatto, P., Rosenthal, G., and M. Przeworski, Natural selection interacts with the local recombination rate to shape the evolution of hybrid genomes. Submitted. On BioRxiv.

2017

Guerra Amorim, C. E., Gao, Z., Baker, Z., Diesel, J. F., Simons, Y. B., Haque, I. S., Pickrell J.+ and M. Przeworski+, 2017 The population genetics of human disease: the case of recessive, lethal mutations. PLoS Genetics 13:e1006915. On BioRxiv+Co-supervised this work

Baker, Z.*, Schumer, M.*, Haba, Y., Holmes, C., Rosenthal, G., and M. Przeworski, 2017 Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. eLife 6:e24133. On BioRxiv*Contributed equally

Chen, C., Qi, H., Shen, Y., Pickrell, J.+, and M. Przeworski+, 2017 Contrasting determinants of mutation rates in human germline and soma. Genetics . On BioRxiv. +Co-supervised this work

Jackson, W. J., Agarwal, I., and I. Pe’er, 2017 2-Way k-Means as a Model for Microbiome samples. Journal of Healthcare Engineering, Article ID 5284145. On BioRxiv.

Mostafavi, H., Berisa, T., Day, F. R., Perry, J. R. B.,  Przeworski, M.and J. Pickrell+, 2017 Identifying genetic variants that affect viability in large cohorts. PloS Biology 15: e2002458. On BioRxiv  & summary in The Conversation. +Co-supervised this work

Nakatsuka N.J.Moorjani P.Rai N.Sarkar B.Tandon A., Patterson N.Bhavani G.S.Girisha K.M.Mustak M.S.Srinivasan S.Kaushik A.Vahab S.A.Jagadeesh S.M.Satyamoorthy K.Singh L.Reich D., and K. Thangaraj 2017 The promise of disease gene discovery in South Asia.  Nature Genetics 49: 1403–1407. On BioRxiv.

Schumer, M., Powell, D., Delclos, P., Squire, M., Cui, R., Andolfatto, P., and G. Rosenthal, 2017 Assortative mating and persistent reproductive isolation in hybrids. PNAS 114:10936-10941.

Zens, K. D., Chen, J. K., Guyer, R. S., Wu, F. L., Cvetkovski, F., Miron, M., and D. L Farber, 2017 Reduced generation of lung tissue–resident memory T cells during infancy. Journal of Experimental Medicine, jem-20170521.

2016

Moorjani, P.*, Gao, Z.*, and M. Przeworski, 2016 Human germline mutation and the erratic evolutionary clock. PLoS Biology 14:e2000744. On BioRxiv. *Contributed equally

Moorjani, P. *, Amorim, C. E. *, Arndt, P., and M. Przeworski, 2016 Variation in the molecular clock of primates. PNAS 113: 10607–10612. Older version on BioRxiv*Contributed equally

Moorjani, P., Sankararaman, S., Fu, Q., Przeworski, M., Patterson, N., and Reich, D., 2016 Dating ancient human samples using the recombination clock. PNAS 113: 5652-7. Older version on BioRxiv.

Schumer, M, and Y. Brandvain, 2016 Determining epistatic selection in admixed populationsMol Ecol. 25: 2577-91.

Gao, Z., Wyman, M. J., Sella, G., and M. Przeworski, 2016 Interpreting the dependence of mutation rates on age and time. PLoS Biology 14(1):e1002355. Older version on ArXiv.

2015

Morton, E., Lynch, J., Froment, A., Lafosse, S., Heyer, E., Przeworski, M., Blekhman, R.+, and L. Segurel+, 2015 Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence. PloS Genetics 11(11): e1005658. On BioRxiv. +Co-supervised this work

, , , , , O., , D., , A., Q., , B., , C., , S., , G., and Stable recombination hotspots in birds. Science 350: 928-32. Earlier version on BioRxiv+Joint first authors

Meyer, W. K.*, Venkat, A.*, Kermany, A., van de Geijn, B., Zhang, S., and M. Przeworski, 2015 Evolutionary history inferred from the de novo assembly of a non-model organism, the blue-eyed black lemur genome. Molecular Ecology 24:4392-4405. *Contributed equally

Williams, A. L., Genovese, G., Dyer, T., Truax, K., Patterson, N., Blangero, J., Reich, D., Przeworski, M., and T2D-GENES Consortium, 2015 Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. eLife Mar 25;4. doi:10.7554/eLife.04637. On BioRxiv.

Gao, Z., Waggoner, D., Stephens, M., Ober, C., and M. Przeworski, 2015 An estimate of the average number of recessive lethal mutations carried by humans. Genetics Feb 18. pii: genetics.114.173351. On ArXiv.

Gao, Z., Przeworski, M., and G. Sella, 2015 Footprints of ancient balancing selection in genetic variation data. Evolution 69:431-46. On ArXiv.

2014

Segurel, L.*, Wyman, M.*, and M. Przeworski, 2014 Determinants of mutation rate variation in the human germline. Annual Reviews of Human Genetics 15: 47-70.  *Contributed equally

Matute D. R., Gavin-Smyth J., and G. Liu, 2014 Variable post-zygotic isolation in Drosophila melanogaster/D. simulans hybridsJ Evol Biol 27: 1691-1705.

Restrepo S., Tabima J. F., Mideros M. F., Grünwald N. J., and D. R. Matute, 2014 Speciation in fungal and oomycete plant pathogens.  Annu Rev Phytopathol 52: 289-316.

Matute, D. R., and J. F. Ayroles, 2014 Hybridization occurs between D. simulans and D. sechellia in the Seychelles archipelago. Journal of Evolutionary Biology 27: 1057-68.

Matute, D. R., and J. Gavin-Smyth, 2014 Fine mapping of dominant X-linked incompatibility alleles in Drosophila hybrids. PLoS Genetics 10: e1004270.

Kermany, AR., Segurel, L., Oliver, T., and M. Przeworski, 2014 TroX: A new method to learn about the genesis of aneuploidy from trisomic products of conception. Bioinformatics 30: 2035-42.

2013

Rabosky, D. L., and Matute, D. R., 2013 Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds. PNAS 110: 15354-15359.

Matute, D. R., 2013 The role of founder effects on the evolution of reproductive isolation. Journal of Evolutionary Biology 26: 2299-2311

Quach, H., Wilson, D., Laval, G., Patin, E., Manry, J., Guibert, J., Barreiro, L. B., Gessain, A., Przeworski, M., and Quintana-Murci, L., 2013 Different Selective Pressures Shape the Evolution of Toll-like Receptors in Human and non-Human Primate Populations. Human Molecular Genetics 22: 4829-40

Segurel, L., Gao, Z., Przeworski, M., 2013 Ancestry runs deeper than blood: the evolutionary history of ABO points to cryptic variation of functional importance. Bioessays 35: 862-7

Matute, D.R., and Harris, A., 2013 The influence of abdominal pigmentation on desiccation resistance and UV resistance in two species of Drosophila. Evolution 67: 2451-60.

Meyer, W.*, Zhang, S.*, Hayakawa, S.,Imai, H., and M. Przeworski, 2013 The convergent evolution of blue iris pigmentation in primates took distinct molecular paths. Am. J. Phys. Anth. 151(3): 398-407. *Contributed equally

Segurel, L., Austerlitz, F., Toupance, B., Gautier, M., Kelley, JL., Pasquet, P., Lonjou, C., Georges, M., Voisin, S., Cruaud, C., Couloux, A., Hegay., T, Aldashev, A., Vitalis, R., Heyer, E., 2013 Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia. Eur J Hum Genet. 21: 1146-1151.

Gavin-Smyth, J. G., Matute, D.R., 2013 Embryonic lethality leads to hybrid male inviability in hybrids between Drosophila melanogaster and D. santomea. Ecology and Evolution 3: 1580-1589.

Segurel, L., 2013 The complex binding of PRDM9. Genome Biology 14: 112.

Leffler, E.M.*, Gao, Z.*, Pfeifer, S.*, Segurel, L.*, Auton, A., Venn, O., Bowden, R., Bontrop, R., Wall, J. D., Sella, G., Donnelly, P., McVean, G.+, Przeworski, M.+, 2013 Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339: 1578-1582. *Contributed equally +Co-supervised this work Abstract PDF.

Older Lab Publications

Perry, GH., Xue, Y., Smith, RS., Meyer, WK., Caliskan, M., Yanez-Cuna, O., Lee, AS., Gutierrez-Arcelus, M., Ober, C., Hollox, EJ., Tyler-Smith, C., Lee, C., 2012 Evolutionary genetics of the human Rh blood group system. Hum Genet. 131: 1205-16.

Rest, JS., Morales, CM., Waldron, JB., Opulente, DA., Fisher, J., Moon, S., Bullaughey, K., Carey, LB., Dedousis, D., 2012 Nonlinear Fitness Consequences of Variation in Expression Level of a Eukaryotic Gene. Mol. Biol. Evol. 30:448–456.

Rest, JS., Bullaughey, K., Morris, GP., Li, WH., 2012 Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. PLoS ONE 7:e32274.

Segurel, L.*, Thompson, E. E.*, Flutre, T., Lovstad, J., Venkat, A., Margulis, S., Moyse, J., Ross, S., Gamble, K., Sella, G., Ober, C.+, and Przeworski, M.+, 2012 The ABO blood group is a trans-species polymorphism in primates. PNAS 109: 18493-18498. *Contributed equally +Co-supervised this work

Bullaughey, K., 2012 Multidimensional adaptive evolution of a feed-forward network and the illusion of compensation. Evolution 67:49-65.

Leffler, E. M., Bullaughey, K.*, Matute, D.*, Meyer, W.*, Segurel, L.*, Venkat, A.*, Andolfatto, P., and M. Przeworski, 2012 Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 10: e1001388. *Contributed equally

Albu, M., Kermany, A.R. and Hickey, D.A., 2012 Recombination reshuffles the genotypic deck, thus accelerating the rate of evolution. Chapter 3 in Rapidly Evolving Genes and Genetic Systems, edited by Rama S. Singh, Jianping Xu, and Rob J. Kulathinal. Oxford University Press.

Auton, A.*, Fledel-Alon, A.*, Pfeifer, S.*, Venn, O.*, Ségurel, L., Street, T., Leffler, E. M., Bowden, R., Ineas, I., Broxholme, J., Humburg, J., Iqbal, Z., Lunter, G., Maller, J., Hernandez, R. D., Melton, S. C., Venkat, A., Nobrega, M., Bontrop, R., Donnelly, P.+, Przeworski, M.+, and G. McVean+, 2012 A fine-scale chimpanzee genetic map from population resequencing data. Science 336: 193-198.*Contributed equally +Co-supervised this work

Kermany, A.R. and Lessard, S., 2012 Effect of epistasis and linkage on the probability of fixation of a new mutant in three-locus models: an ancestral recombination-selection graph approach. Theoretical Population Biology 82:131-45.

Lessard, S. and Kermany, A.R., 2012 Fixation probability in a two-locus model by the ancestral recombination-selection graph. Genetics 190:691-707.

Meyer, W., Arbeithuber, B., Ober, C., Ebner, T., Tiemann-Boege, I., Hudson, R.R.+, and M. Przeworski+, 2012 Evaluating the evidence for transmission distortion in human pedigrees. Genetics 191:215-232. +Co-supervised this work

Bullaughey K., 2011 Changes in selective effects over time facilitate turnover of enhancer sequences. Genetics 187:567-82.

Fledel-Alon A.*, Leffler E.*, Guan Y., Stephens M., Coop G.+ and M. Przeworski+, 2011 Variation in human recombination rates and its genetic determinants. PLoS One, 6(6): e20321. *Contributed equally +Co-supervised this work

Hernandez R. D., Kelley J. L., Elyashiv E., Melton S. C., Auton A., McVean M., 1000 Genomes Project, Sella G.+ and M. Przeworski+, 2011 Classic selective sweeps were rare in recent human evolution. Science 331: 920-924. + Joint senior authors

Przeworski, M., 2011 The golden age of population genetics. Science 331: 547. [Comment on the 10th anniversary of the sequencing of the human genome.]

Segurel, L., Leffler, E. M., and M. Przeworski, 2011 The case of the fickle fingers: How PRDM9 specifies meiotic recombination hotspots in humans. PLoS Biol 9(12): e1001211.

Wilson, D. J., Hernandez R. D., Andolfatto, P. and M. Przeworski, 2011 A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences. PLoS Genet 7(12): e1002395. doi:10.1371/journal.pgen.1002395.

1000 Genomes Project Consortium, 2010 A comprehensive map of common human genetic variation from population resequencing data. Nature 467: 1061-73. [Lab members: Hernandez, R.Kelley, J.L., Melton, S.C., M. Przeworski]

Buard, J., Baudat, F., Grey, C., Fledel-Alon, A., Ober, C., Przeworski, M., Coop, G., and B. de Massy, 2010 The zinc finger protein PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-40.

Elyavish, E., Bullaughey, K., Sattath, S., Rinott, Y., Przeworski, M. and G. Sella, 2010 Variation in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species. Genome Research 20: 1558-1573.

Kelley, J. L., Aagaard, J., MacCoss, M. and W. Swanson, 2010 Functional diversification and evolution of antifreeze proteins in the Antarctic fish Lycodichthys dearborni. Journal of Molecular Evolution, 71: 111-118.

Kosova, G., Pickrell, J. K., Kelley, J. L., McArdle, P. F., Shuldiner, A. R., Abney, M. and C. Ober, 2010 The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. PLoS Genetics 6: e1000974.

Becquet, C., and M. Przeworski, 2009 Learning about modes of speciation from computational approaches. Evolution 63: 2547-62.

Brehony, C., Wilson, D. J. and M. C. J. Maiden, 2009 Variation of the factor-H binding protein of Neisseria meningitidis. Microbiology 155: 4155-69.

Bullaughey, K., Chavarria, C. I., Coop, G. and Y. Gilad, 2009 Expression quantitative trait loci detected in cell-lines are often present in primary tissues. Human Molecular Genetics 18: 4296-303.

Fledel-Alon, A., Wilson, D. J., Broman, K., Wen, X., Ober, C., Coop, G. and M. Przeworski, 2009 Broad-scale recombination patterns underlying proper disjunction in humans. PLoS Genetics 5: e1000658.

Mullner, P., Shadbolt, T., Collins-Emerson, J. M., Midwinter, A. C., Spencer, S. E. F., Marshall, J., Carter, P., Campbell, D. M., Wilson, D. J., Hathaway, S., Pirie, R. and N. P. French, 2009 Molecular and spatial epidemiology of human campylobacteriosis in New Zealand – source association and genotype-related risk factors. Epidemiology and Infection 138: 1372-83.

Mullner, P., Spencer, S. E. F., Wilson, D. J., Jones, G., Noble, A. D., Midwinter, A. C., Collins-Emerson, J. M., Carter, P., Hathaway, S. and N. P. French, 2009 Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach. Infection, Genetics and Evolution 9: 1311-9.

Sella, G., Petrov, D., Przeworski, M. and P. Andolfatto, 2009 Pervasive natural selection in theDrosophila genome? PLoS Genetics 5: e1000495.

Sheppard, S. K., Dallas, J. F., Strachan, N. J. C., MacRae, M., McCarthy, N. D., Wilson, D. J., Gormley, F. J., Falush, D., Ogden, I. D., Maiden, M. C. J. and K. J. Forbes, 2009 Campylobacter genotyping to determine the source of human infection. Clinical Infectious Diseases 48: 1072-8.

Wilson, D. J., Gabriel, E., Leatherbarrow, A. J. H., Cheesbrough, J., Gee, S., Bolton, E., Fox, A., Hart, C. A., Diggle, P. J. and P. Fearnhead, 2009 Rapid evolution and the importance of recombination to the gastro-enteric pathogen Campylobacter jejuni. Molecular Biology and Evolution 26: 385-97.

Blekhman, R., Orna, M., Herrmann, L., Boyko, A., Indap, A., Kosiol, C., Bustamante, C. D., Teshima, K. and M. Przeworski, 2008 Natural selection on genes that underlie human disease susceptibility. Current Biology 18: 883-9.

Bullaughey, K., Przeworski, M.+ and G. Coop+, 2008 No effect of recombination on the efficacy of natural selection in primates. Genome Research 18: 544-54.+Co-supervised this work

Coop, G., Bullaughey, K., Luca, F. and M. Przeworski, 2008 The timing of selection at the human FOXP2 gene. Mol. Biol. Evol 25: 1257-9.

Coop, G., Wen, W., Ober, C., Pritchard, J. K. and M. Przeworski, 2008 High resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science 319: 1395-8.

Hernandez, R. D., 2008 A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24: 2786-7.

Kelley, J. L., Turkheimer, K., Haney, M. and W. J. Swanson, 2008 Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations. Human Molecular Genetics doi: 10.1093/hmg/ddn399.

Wilson, D. J., Gabriel, E., Leatherbarrow, A. J. H., Cheesbrough, J., Gee, S., Bolton, E., Fox, A., Fearnhead, P., Hart, C. A. and P. J. Diggle, 2008 Tracing the source of campylobacteriosis. PLoS Genetics 4: e1000203.

Becquet, C., Patterson, N., Stone, A. C., Przeworski, M.+ and D. Reich+, 2007 Genetic structure of chimpanzee populations. PLoS Genetics 3: e66.+Co-supervised this work

Becquet, C. and M. Przeworski, 2007 A new method to estimate parameters of speciation models, with application to apes. Genome Research 17: 1505-19.

Clark, V. J., Ptak, S. E., Tiemann, I., Qian, Y., Coop, G., Stone, A. C., Przeworski, M., Arnheim, N., and A. Di Rienzo, 2007 Combining sperm typing and linkage disequilibrium analyses reveals differences in selective pressures or recombination rates across human populations. Genetics 175: 795-804.

Coop, G., and M. Przeworski, 2007 An evolutionary view of human recombination. Nat. Rev. Genet. 8: 23-34.

Thornton, K. R., Jensen, J. D., Becquet, C. and P. Andolfatto, 2007 Progress and prospects in mapping recent selection in the genome. Heredity 98: 340-348.

Teshima, K. M., Coop, G. and M. Przeworski, 2006 How reliable are empirical genomic scans for selective sweeps? Genome Res. 16: 702-712.

Teshima, K. M. and M. Przeworski, 2006 Directional selection on alleles of arbitrary dominance. Genetics 172: 713-8.

Tyler-Smith, C. and M. Przeworski, 2006 From genomics and evolution to medicine. Curr. Opin. Genet. Dev. 16: 541-544.

Przeworski, M., Coop, G., and J. D. Wall, 2005 The signature of selection on standing genetic variation. Evolution 59: 2312-2323.

Rompler, H., Schulz, A., Pitra, C., Coop, G., Przeworski, M., Pääbo, S., and T. Schöneberg, 2005 The rise and fall of the chemoattractant receptor GPR33. J.B.C. 280: 31068-75.

Ptak, S. E., Hinds, D. A., Koehler, K., Nickel, B., Patil, N. Ballinger, N., Przeworski, M.+, Frazer, K.,+and S. Pääbo+, 2005 Fine-scale recombination patterns differ between chimpanzees and humans. Nat. Genet. 37: 429-434. +Contributed equally

Przeworski, M., 2005 Motivating hotspots. Science 310:247-248. [Comment on a research paper by Myers et al.]

Przeworski, M. and C. D. Bustamante, 2005 Genetic signatures of natural selection. Chapter in Encyclopedia of Genomics, Proteomics and Bioinformatics.

Fischer, A., Wiebe, V., Pääbo, S., and M. Przeworski, 2004 Evidence for a complex demographic history of chimpanzees. Mol. Biol. Evol. 21: 799-808.

Gilad, Y., Przeworski, M., and Lancet, D., 2004 Loss of olfactory gene receptors coupled to the acquisition of full trichromatic vision in primates. PloS Biology 2: 120-125. See erratum in PLoS Biol. 2007 5:e148.

Ptak, S. E., Roeder, A., Stephens, M., Gilad, Y., Pääbo, S., and M. Przeworski, 2004 Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biology 2: 849-855.

Ptak, S. E., Voelpel, K., and M. Przeworski, 2004 Insights into recombination from patterns of linkage disequilibrium in humans. Genetics 167: 387-397.

Hellmann, I., Ebersberger, I., Ptak, S., Pääbo, S. and M. Przeworski, 2003 A neutral explanation for the correlation between diversity levels and recombination rates in humans. Am. J. Hum. Gen. 72: 1527-35.

Przeworski, M., 2003 Estimating the time since fixation of a beneficial allele. Genetics 164: 167-176.

Enard, W., Przeworski, M., Fisher, S. E., Lai, C. S. L., Wiebe V., Kitano, T., Monaco, A. P. and S. Pääbo, 2002 Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869-871.

Gilad, Y., Rosenberg, S., Przeworski, M., Lancet, D. and K. Skorecki, 2002 Evidence for positive selection and population structure at the human MAO-A gene. Proc. Natl. Acad. Sci. 99: 862-867.

Ptak, S., and M. Przeworski, 2002 Evidence for population growth in humans is confounded by population structure. Trends in Gen.18: 559-563.

From PhD/Postdoc

Przeworski, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.

Wall, J. D., P. Andolfatto and M. Przeworski, 2002 Testing models of selection and demography in Drosophila simulans. Genetics 162: 203-216.

Andolfatto, P., and M. Przeworski, 2001 Regions of lower recombination harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158: 657-665.

Pritchard, J. K., and M. Przeworski, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Gen. 68: 1-14.

Przeworski, M., and J. D. Wall, 2001 Why is there so little intragenic linkage disequilibrium in humans? Genetical Research 77:143-151.

Przeworski, M., J. D. Wall, and P. Andolfatto, 2001 Recombination and the frequency spectrum inDrosophila melanogaster and D. simulans. Mol. Biol. Evol. 18: 291-298.

Andolfatto, P., and M. Przeworski, 2000 A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 155: 257-268.

Przeworski, M., Hudson, R. R., and A. Di Rienzo, 2000 Adjusting the focus on human variation. Trends in Gen.16: 296-302.

Wall, J. D., and M. Przeworski, 2000 When did the human population start increasing? Genetics 155: 1865-1874.

Przeworski, M., Charlesworth, B., and J. D. Wall, 1999 Genealogies and weak purifying selection. Mol. Biol. Evol. 16: 246-252.

Przeworski, M., and J. D. Wall, 1999 An evaluation of a hierarchical birth-death process as a model for species diversification. Paleobiology 24: 498-511.