Publications
I’ve given links, pdfs of the main text and supplementary material, and talk slides< and posters where available.
Graham’s pubmed list of publications, and a google scholar list. Graham’s BioRxiv & arXiv feeds are here and here.
* – denotes an equal contribution. Bold shows folks who were part of the Coop lab when work was done.
In the works
The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data Vince Buffalo, Graham Coop. bioRxived.
Attacks on genetic privacy via uploads to genealogical databases Michael D Edge, Graham Coop Elife preprint. blog post.
2019
Donnelly (1983) and the limits of genetic genealogy Michael D. Edge, Graham Coop. Theo. Pop. Bio. pdf Donnelly & Thompson commentaries
Population genomics perspectives on convergent adaptation Kristin M Lee, Graham Coop Phil. Trans. Royal Soc. B bioRxived
Reduced signal for polygenic adaptation of height in UK Biobank. Jeremy J Berg, Arbel Harpak, Nicholas Sinnott-Armstrong, Anja Moltke Joergensen, Hakhamanesh Mostafavi, Yair Field, Evan A Boyle, Xinjun Zhang, Fernando Racimo, Jonathan K Pritchard, Graham Coop. eLife. bioRxived
Adaptive introgression enables evolutionary rescue from extreme environmental pollution Elias M. Oziolor Noah M. Reid, Sivan Yair, Kristin M. Lee, Sarah Guberman VerPloeg, Peter C. Bruns, Joseph R. Shaw, Andrew Whitehead, Cole W. Matson. Science.
How lucky was the genetic investigation in the Golden State Killer case? Michael Edge, Graham Coop. . This was originally a blog post, bioRxiv version to allow more easy citation.
Detecting adaptive differentiation in structured populations with genomic data and common gardens Emily B Josephs, Jeremy J. Berg, Jeffrey Ross-Ibarra, Graham Coop. Genetics bioRxived
2018
Allele frequency dynamics in a pedigreed natural population Nancy Chen, Ivan Juric, Elissa J. Cosgrove, Reed Bowman, John W. Fitzpatrick, Stephan J. Schoech, Andrew G. Clark, Graham Coop. PNAS bioRxived. PNAS Perspective on work.
Reconstructing the history of polygenic scores using coalescent trees Michael D. Edge and Graham Coop. Genetics bioRxived
Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Noah A Rosenberg, Michael D Edge, Jonathan K Pritchard, Marcus W Feldman. Evolution, Medicine, and Public Health.
Inferring Continuous and Discrete Population Genetic Structure Across Space Gideon Bradburd, Graham Coop, Peter Ralph. Genetics BioRxived.
Estimating time to the common ancestor for a beneficial allele. Joel Smith, Graham Coop, Matthew Stephens, John Novembre. MBE BioRxived.
2017
Distinguishing among modes of convergent adaptation using population genomic data Kristin M Lee, Graham Coop. BioRxived
Polygenic Adaptation has Impacted Multiple Anthropometric Traits. Jeremy J Berg, Xinjun Zhang, Graham Coop BioRxived. Note: see Berg et al. for our discussion of replication issues.
Population-genomic inference of the strength and timing of selection against gene flow. Simon Aeschbacher, Jessica Packard Selby, John H. Willis, Graham Coop. PNAS BioRxived.
Deconstructing isolation-by-distance: the genomic consequences of limited dispersal. Stepfanie Aguillon, John W. Fitzpatrick, Reed Bowman, Stephan J. Schoech, Andrew G. Clark, Graham Coop*, Nancy Chen* PLOS Genetics BioRxived Cover image
Inferring recent demography from isolation by distance of long shared sequence blocks. Harald Ringbauer, Graham Coop, Nick Barton. Genetics. BioRxived.
2016
The Strength of Selection Against Neanderthal Introgression. Ivan Juric, Simon Aeschbacher, Graham Coop. PLOS Genetics. bioRxived.
A genomic map of the effects of linked selection in Drosophila. Eyal Elyashiv, Shmuel Sattath, Tina T. Hu, Alon Strustovsky, Graham McVicker, Peter Andolfatto, Graham Coop, Guy Sella. PLOS Genetics. ArXived. Commentary piece
A Genealogical Look at Shared Ancestry on the X Chromosome Vince Buffalo, Stephen M. Mount, Graham Coop Genetics. bioRxiv. blog post. Vince’s talk
The evolution of genomic islands by increased establishment probability of linked alleles. Molecular Ecology. Sam Yeaman, Simon Aeschbacher, Reinhard Bürger.
A Spatial Framework for Understanding Population Structure and Admixture. Gideon Bradburd, Peter L. Ralph, Graham Coop. PLOS Genetics. bioRxiv.
Does linked selection explain the narrow range of genetic diversity across species? Graham Coop. bioRxived.
2015
Convergent Evolution During Local Adaptation to Patchy Landscapes Peter L. Ralph, Graham Coop. PLOS Genetics. bioRxived.
Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic variation Kevin M. Wright, Uffe Hellsten, Chenling Xu, Annie L. Jeong, Avinash Sreedasyam, Jarrod A. Chapman, Jeremy Schmutz, Graham Coop, Daniel S. Rokhsar, John H. Willis. bioRxived
The role of standing variation in geographic convergent adaptation. Peter L. Ralph, Graham Coop. Am.Nat. bioRxived.
A Coalescent Model of a Sweep from a Uniquely Derived Standing Variant. Jeremy J Berg, Graham Coop. Genetics. bioRxived
The Spatial Mixing of Genomes in Secondary Contact Zones Alisa Sedghifar, Yaniv Brandvain, Peter L. Ralph, Graham Coop Genetics. bioRxived.
Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation Christopher H. Martin, Joseph S. Cutler, John P. Friel, Cyrille T. Dening, Graham Coop, Peter C. Wainwright. Evolution. pdf.
Sperm should evolve to make female meiosis fair. Yaniv Brandvain, Graham Coop. Evolution. bioRxived
2014
Isolation by environment. Ian Wang* and Gideon Bradburd* 2014 Molecular Ecology.
Speciation and introgression between Mimulus nasutus and Mimulus guttatus. Yaniv Brandvain*, Amanda M. Kenney*, Lex Flagel, Graham Coop*, Andrea L Sweigart*. PLOS Genetics. arXived here.
A Population Genetic Signature of Polygenic Local Adaptation Berg, JJ and Coop G. PLOS Genetics. 2014 arXived here. Blog posts here and here. Some comments here. CODE.
2013
Genomic identification of founding haplotypes reveals the
history of the selfing species Capsella rubella Brandvain Y, Slotte T, Hazzouri KM, Wright SI, Coop G. arXived here.
Disentangling the effects of geographic and ecological isolation on genetic differentiation Bradburd G, Ralph P, Coop G Evolution. arXiv
[code, BEDAZZLE]
Robust identification of local adaptation from allele frequencies. Torsten Günther, Graham Coop Genetics 2013 arXived here Work done while Torsten was visiting student to Davis. [code, Bayenv2.0]
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo Y, Steige K, Platt AD, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Prochnick S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI. Nature Genetics.
The geography of recent genetic ancestry across Europe. Ralph PL and Coop G.. PLOS Biology ArXiv. Peter’s SMBE Poster and CIRM talk, see here for some links to press coverage, and our FAQ on the points raised by the article. [code]
2012
Patterns of neutral diversity under general models of selective sweeps. Coop G. and Ralph PL. Genetics 2012. ArXiv, Supp. R code, (slides, poster, blog post)
Scrambling Eggs: Meiotic drive and the evolution of sex-specific recombination. Brandvain Y. and Coop G. Genetics. 2012. Arxiv. blog posts
Inbreeding and haploid chromosomes: a response to Hedrick Evolution. 2012. Brandvain Y , Wade MJ.
Is your phylogeny informative? Measuring the power of comparative methods. Boettiger C, Coop G, Ralph PL to appear Evolution 2012 Arxived Arxiv code, (Carl’s slides, blog posts.
Stochastic population growth in spatially heterogeneous environments.
Evans SN, Ralph PL, Schreiber SJ, Sen A, Journal Math. Bio., 2012 Arxiv
2011
Demography, kinship, and the evolving theory of genomic imprinting. Brandvain, Y., J. Van Cleve, F. Ubeda, and J.F. Wilkins. Trends in Genetics 2011.
Transcriptional regulation: effects of promoter proximal pausing on speed, synchrony and reliability.Boettiger AN, Ralph PL, Evans SN. PLoS Computational Biology 2011
Horizontal transmission rapidly erodes disequilibria between organelle and symbiont genomes. Brandvain, Y., C. J. Goodnight, and M. J. Wade. Genetics. 2011.
Variation in human recombination rates and its genetic determinants. Fledel-Alon A, Leffler EM, Guan Y, Stephens M, Coop G*, Przeworski M.*. PLoS One 2011
Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Eckert AJ, Bower AD, González-Martínez SC, Wegrzyn JL, Coop G, Neale DB. Molecular Ecology 2011
2010
Parallel adaptation: One or many waves of advance of an advantageous allele? Ralph PL, Coop G. Genetics 2010. (blog reviews: John Hawks, Luke Jostin and Danny Wilson. Faculty 1000 reviews by John Novembre and Stephen Wright)
Using Environmental Correlations to Identify Loci Underlying Local Adaptation. Coop G., Witonsky D., Di Rienzo A., Pritchard J.K. Genetics. 2010
Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency 1. Hancock AM, Witonsky D, Ehler E, Alkorta-Aranburu G, Beall C, Amha Gebremedhin,Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo PNAS 2010
The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Prichard JK, Pickrell JK, Coop G. Current Biology. 2010
PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice . Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, Przeworski M, Coop G, de Massy B (2010) Science. See also the papers by
Myers et al. and Parvanov et al. that appeared in the same issue.
2009
Broad-Scale Recombination Patterns Underlying Proper Disjunction in Humans
Fledel-Alon A, Wilson DJ, Broman K, Wen X, Ober C, Coop G*, Przeworski M.* (2009) PLoS Genetics
Expression quantitative trait loci detected in cell lines are often present in primary tissues. Bullaughey K, Chavarria CI, Coop G*, Gilad Y.* (2009) Hum Mol Genet. pdf
The role of geography in human adaptation Coop G*, Pickrell JK*, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK. (2009) PLoS Genetics
Signals of recent positive selection in a worldwide sample of human populations. Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li J, Absher D, Srinivasan B, Barsh GS, Myers RM, Feldman MW, Pritchard JK. (2009) Genome Research
An approximate likelihood for genetic data under a model with recombination and population splitting Davison D, Pritchard JK, Coop G. (2009) Theor. Pop. Bio.
2008
The timing of selection at the human FOXP2 gene. Coop, G., Bullaughey, K., Luca, F., and M. Przeworski, 2008 Mol Biol Evol.25(7):1257-9 pdf , Supplementary info.
Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Pemberton TJ, Jakobsson M, Conrad DF, Coop G, Wall JD, Pritchard JK, Patel PI, Rosenberg NA. 2008 Ann Hum Genet. 72:535-46
No effect of recombination on the efficacy of natural selection in primates. Bullaughey K, Przeworski M*, Coop G* 2008 Genome Research. pdf , Supplementary info.
High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Coop G, Wen X, Ober C, Pritchard JK, Przeworski M. Science, 2008, pdf , Slides, Data
Adaptations to Climate in Candidate Genes for Common Metabolic Disorders. Hancock MA, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G, Di Rienzo A PLoS Genetics 2008.
2007
Adaptive drool in the gene pool Novembre J*, Pritchard JK, Coop G*, Nature Genetics, 2007
Live Hot, Die Young: Transmission Distortion in Recombination Hotspots Coop G*, Myers S*, PLoS Genetics, 2007 pdf , Slides
An evolutionary view of human recombination. Coop G, Przeworski M. Nat Rev Gen, 2007 pdf
2006
Sequencing and analysis of Neanderthal genomic DNA. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Paabo S, Pritchard JK, Rubin EM. Science. 2006, 314:1113-8. pdf , Slides
How reliable are empirical genomic scans for selective sweeps? Teshima KM, Coop G, Przeworski M., Genome Res. 2006 (selected by Faculty of 1000) pdf
A worldwide survey of haplotype variation and linkage disequilibrium in the human genome Conrad DF*, Jakobsson M*, Coop G*, Wen X, Wall JD, Rosenberg NA, Pritchard JK., Nat Gen 2006 pdf
Combining sperm typing and LD analyses reveals differences in selective pressures or recombination rates across human populations. Clark V, Ptak SE, Tiemann-Boege I, Qian Y, Coop G, Stone AC, Przeworski M, Arnheim N, Di Rienzo A. Genetics. 2006 pdf
Screening for recently selected alleles by analysis of human haplotype similarity. Hanchard NA, Rockett KA, Spencer C, Coop G, Pinder M, Jallow M, Kimber M, McVean G, Mott R, Kwiatkowski DP. American Journal of Human Genetics, 2006 Jan;78(1):153-9
Spread of an Inactive Form of Caspase-12 in Humans Is Due to Recent Positive Selection Yali Xue, Allan Daly, Bryndis Yngvadottir, Mengning Liu, Graham Coop, Yuseob Kim, Pardis Sabeti, Yuan Chen, Jim Stalker, Elizabeth Huckle, John Burton, Steven Leonard, Jane Rogers, and Chris Tyler-Smith. American Journal of Human Genetics, 2006, Apr;78(4):659-70
2005
The signature of positive selection on standing genetic variation. Przeworski M, Coop G, Wall JD. Evolution 2005. pdf
Can a genome change its (hot)spots. Coop G. Trends in Ecology and Evolution. Dec 2005; 20 (12), 643-645 pdf
The rise and fall of the chemoattractant receptor GPR33. Rompler H, Schulz A, Pitra C, Coop G, Przeworski M, Paabo S, Schoneberg T. J Biol Chem. 2005, PubMed
2004
SelSim: a program to simulate population genetic data with natural selection and recombination. Spencer C.C.A., Coop G. Bioinformatics. Jul 2004, 22 pdf
Darwinian Selection on a Selfing Locus.
Shimizu KK, Cork JM, Caicedo AL, Mays CA, Moore RC, Olsen KM, Ruzsa S, Coop G, Bustamante CD, Awadalla P, Purugganan MD. Science. 2004, 306 (5704), 2081-4. pdf This article was later retracted due to PCR errors;
Ancestral inference on gene trees under selection.
Coop G. , Griffiths R. C., Theor Popul Biol, Nov 2004; 66 (3); 219-32. pdf ; (selected by Faculty of 1000)
The Likelihood of Gene Trees under Selective Models. Coop G., DPhil. Thesis, 2004. Coop DPhil (PhD)_thesis
gcbias 