Research Topics
Genomes and GenesSpecies | Graham CoopSummaryAffiliation: University of California Country: USA Publications
| Collaborators
|
Detail Information
Publications
Patterns of neutral diversity under general models of selective sweepsGraham Coop
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95616, USA
Genetics 192:205-24. 2012..The general model of selective sweeps we describe goes some way toward providing a more flexible framework to describe genomic patterns of diversity than is currently available...- The role of geography in human adaptationGraham Coop
Department of Human Genetics, University of Chicago, Chicago, IL, USA
PLoS Genet 5:e1000500. 2009..These patterns suggest that selection is often weak enough that neutral processes -- especially population history, migration, and drift -- exert powerful influences over the fate and geographic distribution of selected alleles... - Using environmental correlations to identify loci underlying local adaptationGraham Coop
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, Calfornia 95616, USA
Genetics 185:1411-23. 2010..Software is available at http://www.eve.ucdavis.edu/gmcoop/... - Adaptations to climate-mediated selective pressures in humansAngela M Hancock
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 7:e1001375. 2011..Further, we find an enrichment of strong signals in gene sets related to UV radiation, infection and immunity, and cancer. Our results imply that adaptations to climate shaped the spatial distribution of variation in humans... 
High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humansGraham Coop
Department of Human Genetics, University of Chicago, 920 East 58th Street, Cummings Life Science Center, Chicago, IL 60637, USA
Science 319:1395-8. 2008..Notably, however, we found extensive and heritable variation among both males and females in the proportion of crossovers occurring in these hotspots...- Signals of recent positive selection in a worldwide sample of human populationsJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Res 19:826-37. 2009..Finally, we search for local adaptation between geographically close populations, and highlight several examples... - Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)Andrew J Eckert
Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
Mol Ecol 19:3789-805. 2010.... - Live hot, die young: transmission distortion in recombination hotspotsGraham Coop
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 3:e35. 2007..We explore the impact of hotspot alleles on patterns of haplotype variation, and show that such alleles mask their presence in population genetic data, making them difficult to detect... - Combining sperm typing and linkage disequilibrium analyses reveals differences in selective pressures or recombination rates across human populationsVanessa J Clark
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genetics 175:795-804. 2007.... - Adaptations to climate in candidate genes for common metabolic disordersAngela M Hancock
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 4:e32. 2008..Nevertheless, our results are consistent with the idea that climate has been an important selective pressure acting on candidate genes for common metabolic disorders... - Broad-scale recombination patterns underlying proper disjunction in humansAdi Fledel-Alon
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 5:e1000658. 2009..These findings point to multiple mechanisms that shape the distribution of crossovers, influencing proper disjunction in humans... - Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequencyAngela M Hancock
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 107:8924-30. 2010.... - No effect of recombination on the efficacy of natural selection in primatesKevin Bullaughey
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 18:544-54. 2008..An interesting implication is that indirect selection for recombination modifiers has probably been a weak force in primate evolution... 
A worldwide survey of haplotype variation and linkage disequilibrium in the human genomeDonald F Conrad
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Genet 38:1251-60. 2006..Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations...- An evolutionary view of human recombinationGraham Coop
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Rev Genet 8:23-34. 2007.... - Variation in human recombination rates and its genetic determinantsAdi Fledel-Alon
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS ONE 6:e20321. 2011..SIGNIFICANCE: These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes... - Is your phylogeny informative? Measuring the power of comparative methodsCarl Boettiger
Center for Population Biology, University of California, Davis, California 95616, USA
Evolution 66:2240-51. 2012..We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods... - Scrambling eggs: meiotic drive and the evolution of female recombination ratesYaniv Brandvain
Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616, USA
Genetics 190:709-23. 2012..We discuss how selection to modify the efficacy of meiotic drive may contribute to commonly observed patterns of sex differences in recombination... - The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptationJonathan K Pritchard
Department of Human Genetics, The University of Chicago, Room 507, 929 E 58th St, Chicago, IL 60637, USA
Curr Biol 20:R208-15. 2010..We close by discussing some of the likely opportunities for progress in the field... - Parallel adaptation: one or many waves of advance of an advantageous allele?Peter Ralph
Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
Genetics 186:647-68. 2010..Thus, we predict that as more data become available, many more examples of intraspecies parallel adaptation will be uncovered... - Expression quantitative trait loci detected in cell lines are often present in primary tissuesKevin Bullaughey
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
Hum Mol Genet 18:4296-303. 2009..Our results indicate that functional studies in cell lines may uncover a substantial amount of genetic variation that affects gene expression levels in human primary tissues... - How reliable are empirical genomic scans for selective sweeps?Kosuke M Teshima
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 16:702-12. 2006..g., the dominance coefficient) affect the power to detect targets of selection, genomic scans will yield an unrepresentative subset of loci that contribute to adaptations... - The signature of positive selection on standing genetic variationMolly Przeworski
Department of Human Genetics, University of Chicago, Illinois 60637, USA
Evolution 59:2312-23. 2005..These findings highlight the importance of an accurate characterization of the effects of positive selection, if we are to reliably identify recent adaptations from polymorphism data...