Publications

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 arXiv feed is here.

* – denotes an equal contribution

In the works

The role of standing variation in geographic convergent adaptation. Peter L. Ralph, Graham Coop. 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. ARxived.

Convergent Evolution During Local Adaptation to Patchy Landscapes Peter L. Ralph, Graham Coop. bioRxived.

Sperm should evolve to make female meiosis fair. Yaniv Brandvain, Graham Coop bioRxived.

2014


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. pdf