Publications

List of Publications:

20172016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |

For citation statistics and metrics, see: Google Scholar or  ISI.

Pub Med Publication Search all years | 2015 | 2014 | 2013 | 2012


2017

Josephs, E.B., J.R. Stinchcombe, and S.I. Wright. What can genome-wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?  New Phytologist 214: 21-33[pdf]

McGoey, B.V., R. Janik, and J.R. Stinchcombe. 2017. Individual chambers for controlling crosses in wind pollinated plants. Methods in Ecology and Evolution[pdf]

Gould, B.A. and J.R. Stinchcombe. 2017. Population genomic scans suggest novel genes underlie convergent flowering time evolution in the introduced range of Arabidopsis thaliana.  Molecular Ecology  26: 92-106. [pdf]


2016

Sicard, A., C. Kappel, Y.W. Lee, N.J. Woźniaka, C. Marona, J.R. Stinchcombe, S.I. Wright, and M. Lenhard. Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution in Capsella. PNAS 113: 13911-13916. [pdf]

Grillo, M.A., J.R. Stinchcombe, and K.D. Heath. 2016. Nitrogen addition does not influence pre-infection partner choice in the legume-rhizobium symbiosis. American Journal of Botany 103: 1763-1770. [pdf]

Afkhami, M.E. and J.R. Stinchcombe. 2016. Multiple mutualist effects on genome-wide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria, and mycorrhizal fungi. Molecular Ecology 25: 4946-4962.[pdf]

Weiß, C.L., V.J. Schuenemann, J. Davos, G. Shirsekar, E. Reiter, B.A. Gould, J.R. Stinchcombe, J. Krause, and H.A. Burbano. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. Royal Society Open Science 3: 160239. [pdf]

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2015

Huang, Y., J.R. Stinchcombe and A.F. Agrawal. 2015. Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity. Evolution 69, no. 10 (2015): 2735-2746. [pdf]

Sicard, A., C. Kappel, E.B. Josephs, Y.W. Lee, C. Marona, J.R. Stinchcombe, S.I. Wright and M. Lenhard. 2015. Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in CapsellaNature communications 6 (2015). [pdf]

Simonsen, A.K., S. Han, P. Rekret, C.S. Rentschler, K.D. Heath and J.R. Stinchcombe. 2015. Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria. PeerJ 3 (2015): e1291.  [pdf]

Josephs, E.B., Y.W. Lee, J.R. Stinchcombe and S.I. Wright.  2015. Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression.  Proceedings of the National Academy of Sciences 112: 15390-15395.  [pdf]

Kingsolver, J.G., N. Heckman, J. Zhang, P.A. Carter, J.L Knies, J.R. Stinchcombe and K. Meyer. 2015. Genetic variation, simplicity, and evolutionary constraints for function-valued traits. American Naturalist. 185, No. 6 (June 2015), pp. E166-E181
[pdf] [On-line Supplementary Data]

Stock, A.J., B.V. McGoey and J.R. Stinchcombe. 2015. Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution. PeerJ. 3: e898[pdf] [On-line Supplementary Data]

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2014

Simonsen, A.K. and J.R. Stinchcombe. 2014. Standing genetic variation in host preference for mutualist microbial symbionts. Proc Roy Soc B. 281: 20142036.
[pdf[On-line Supplementary Data]

Simonsen, A.K., T. Chow, and J.R. Stinchcombe. 2014. Reduced plant competition amongst kin can be explained by Jensen’s inequality. Ecology and Evolution. 4: 4454-4466.
[pdf[On-line Supplementary Data]

Sicard, A., A. Thamm, C. Marona, Y.W. Lee, V. Wahl, J.R. Stinchcombe, S.I. Wright, C. Kappel, and M. Lenhard. 2014. Repeated evolutionary changes of leaf morphology caused by mutations to a homebox gene. Current Biology 24: 1880-1886.
[pdf] [On-line Supplementary Data]

Stock, A.J., B.E. Campitelli and J.R. Stinchcombe. 2014. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea. Phil. Trans. R. Soc. B 369: 20130259; doi:10.1098/rstb.2013.0259
[pdf] [On-line Supplementary Data]

Campitelli, B.E. and J.R. Stinchcombe. 2014. Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America. G3: Genes, Genomes, Genetics 4: 1407-1416 . doi:10.1534/g3.114.011700
[pdf] [On-line Supplementary Data]

Stinchcombe, J.R. 2014. Cross-pollination of plants and animals: wild quantitative genetics and plant evolutionary genetics. Pages 128- 146, in A. Charmantier, D. Garant, and L.E.B. Kruuk, eds., Quantitative Genetics in the Wild, Oxford University Press, Oxford, U.K.
[pdf][Purchase a copy of the book here]

Stinchcombe, J.R., Simonsen, A.K., and M.W. Blows. 2014. Estimating uncertainty in multivariate responses to selection. Evolution 68: 1188-1196. DOI: 10.1111/evo.12321
[pdf] [On-line Supplementary Data]

Lee, Y.W., B.A. Gould, and J.R. Stinchcombe. 2014. Identifying the genes underlying quantitative traits: A rationale for the QTN programme. AoB Plants 6: plu004 . DOI:10.1093/aobpla/plu004
[pdf]

Simonsen, A.K. and J.R. Stinchcombe 2014. Herbivory eliminates fitness costs of mutualism exploiters. New Phytologist 202: 651-661. DOI: 10.1111/nph.12668
[pdf] [On-line Supplementary Data]

Heath, K.D. and J.R. Stinchcombe. 2014. Explaining mutualism variation: A new evolutionary paradox? Evolution 68: 309-317. DOI: 10.1111/evo.12292
[pdf]

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2013

Campitelli, B.E., A.J. Gorton, K.L. Ostevik, and J.R. Stinchcombe. 2013. The effect of leaf shape on the thermoregulation and frost tolerance of an annual vine. American Journal of Botany 100: 2175-2182.
[pdf] [On-line Supplementary Data]

Wyman, M.J., J.R. Stinchcombe, and L. Rowe. 2013. A multivariate view of the evolution of sexual dimorphism. Journal of Evolutionary Biology 26: 2070-2080. DOI: 10.1111/jeb.12188
[pdf]

Haudry, A., A.E. Platts, E. Vello, D.R. Hoen, M. Leclerq, R.J. Williamson, E. Forczek, Z. Joly-Lopez, J.G. Steffen, K.M. Hazzouri, K. Dewar, J.R. Stinchcombe, D.J. Schoen, X. Wang, J. Schmutz, C.D. Town, P.P. Edger, J.C. Pires, K.S. Schumaker, D.E. Jarvis, T. Mandakova, M.A. Lysak, E. van den Bergh, M.E. Schranz, P.M. harrison, A.M. Moses, T.E. Bureau, S.I. Wright, M. Blanchette. 2013. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature Genetics 45: 891-898. DOI:10.1038/ng.2684
[pdf] [On-Line Supporting Information]

Campitelli, B.E. and J. R. Stinchcombe. 2013. Testing potential selective agents acting on leaf shape in Ipomoea hederacea: predictions based on an adaptive leaf shape cline. Ecology and Evolution 3: 2409-2423. DOI: 10.1002/ece3.641
[pdf] [On-Line Supporting Information] [Data on Dryad]

Gaydos, T.L., N.E. Heckman, M. Kirkpatrick, J.R. Stinchcombe, J. Schmitt, J. Kingsolver, J.S. Marron. 2013. Visualizing genetic constraints. Annals of Applied Statistics 7: 860-882.
[pdf]

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2012

Stinchcombe, J.R., Function-valued Traits Working Group, and M. Kirkpatrick. 2012. Genetics and evolution of function-valued traits: understanding environmentally responsive phenotypes. Trends in Ecology and Evolution 27: 637-647 .
[pdf]

Gorton, A.J., K.D. Heath, M-L. Pilet-Nayel, A. Baranger, and J.R. Stinchcombe. 2012. Mapping the genetic basis of symbiotic variation in legume-rhizobium interactions in Medicago truncatula. G3: Genes, Genomes, Genetics 2: 1291-1303 .
[pdf] [On-Line Supporting Information]

Campitelli, B.E. and J.R. Stinchcombe. 2012. Natural selection maintains a single-locus leaf shape cline in Ivyleaf morning glory, Ipomoea hederacea. Molecular Ecology 21: 552-564.
[pdf] [On-Line Supporting Information]

Heath, K.D., P.V. Burke, and J.R. Stinchcombe. 2012. Coevolutionary genetic variation in the legume-rhizobium transcriptome. Molecular Ecology 21: 4735-4747.
[pdf] [On-Line Supporting Information] [Perspective by Simms & Porter]

Samis, K.E., C.J. Murren, O. Bossdorf, K. Donohue, C.B. Fenster, R.L. Malmberg, M.D. Purugganan, and J.R. Stinchcombe. 2012. Longitudinal trends in climate drive flowering time clines in North Amerian Arabidopsis thaliana. Ecology and Evolution 2: 1162-1180.
[pdf] [On-Line Supporting Information]

von Wettberg, E.J.B., J. R. Stinchcombe, and J. Schmitt. 2012. Early developmental responses to seedling environment modulate later plasticity to light spectral quality. PloS One 7: e34121.
[pdf]

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2011

Baucom, R.S., S-M. Chang, J.M. Kniskern, M.D. Rausher, and J. R. Stinchcombe. 2011. Morning glory as a powerful model in ecological genomics: tracing adaptation through both natural and artificial selection. Heredity 107: 377-385 .
[pdf]

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2010

Brock, M.T., J.M. Dechaine, F.L. Iniguez-Luy, J.N. Maloof, J.R. Stinchcombe, and C. Weinig. 2010. Floral genetic architecture: An examination of QTL architecture underlying floral (co)variation across environments. Genetics 186: 1451-1465.
[pdf] [On-Line Supporting Information]

Heath, K.D., A.J. Stock, and J.R. Stinchcombe. 2010. Mutualism variation in the nodulation response to nitrate. Journal of Evolutionary Biology 23: 2494-2500.
[pdf] [On-Line Supporting Information]

Simonsen, A. K. and J.R. Stinchcombe. 2010. Quantifying evolutionary genetic constraints in the Ivyleaf morning glory, Ipomoea hederacea. International Journal of Plant Sciences 171: 972-986.
[pdf]

Stinchcombe, J.R.. 2010. Ecology and evolution on the banks of the St. Lawrence . New Phytologist 187: 892-894 .
[pdf]

Stinchcombe, J.R., R. Izem, M.S. Heschel, B.V. McGoey, and J. Schmitt. 2010. Across-environment genetic correlations and the frequency of selective environments shape the evolutionary dynamics of growth rate in Impatiens capensis. Evolution 64: 2887-2903.
[pdf] [On-Line Supporting Information]

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2009

McGoey, B.V. and J.R. Stinchcombe. 2009. Interspecific competition alters natural selection on shade avoidance phenotypes in Impatiens capensis. New Phytologist 183: 880-891.
[pdf]

Brock, M.T., J.R. Stinchcombe, and C. Weinig. Indirect effects of FRIGIDA: floral trait (co)variances are altered by seasonally variable abiotic factors associated with flowering time. Journal of Evolutionary Biology 22: 1826-1838.
[pdf]

Stinchcombe, J.R., C. Weinig, K.D. Heath, M.T. Brock, and J. Schmitt. 2009. Polymorphic genes of major effect: consequences for variation, selection, and evolution. Genetics 182: 911-922.
[pdf]

Johnson, M.T.J., M. Vellend, and J.R. Stinchcombe. 2009. Evolution in plant populations as a driver of ecological changes in arthropod communities. Philosophical Transactions of the Royal Society of London B 364, 1593-1605.
[pdf] [Supplemental Data]

Agrawal, A.F. and J.R. Stinchcombe. 2009. How much do genetic covariances alter the rate of adaptation? Proceedings of the Royal Society of London B 276: 1183-1191.
[pdf] [Supplemental Data]

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2008

McKay, J.K. and J.R. Stinchcombe. 2008. Ecological genomics of model eukaryotes. Evolution 62: 2953-2957.
[pdf]

Samis, K.E., K.D. Heath, and J.R. Stinchcombe 2008. Discordant longitudinal clines in flowering time and PHYTOCHROME C in Arabidopsis thaliana. Evolution 62: 2971-2983.
[pdf] [Supplemental Data]

J.R. Stinchcombe, A.F. Agrawal, P. Hohenlohe, S.J. Arnold, and M.W. Blows. 2008. Estimating nonlinear selection gradients using quadratic regression coefficients: double or nothing? Evolution 62: 2435-2440.
[pdf]

Hopkins, R., J. Schmitt, and J.R. Stinchcombe 2008. A latitudinal cline and response to vernalization in leaf angle and morphology in Arabidopsis thaliana (Brassicaceae). New Phytologist 179: 155-164.
[pdf]

Stinchcombe, J.R. and H.E Hoekstra. 2008. Population genomics and quantitative genetics: combined approaches for finding the genes underlying ecologically important traits. Heredity 100: 158-170.
[pdf]

Campitelli, B.E., I. Stehlik, and J.R. Stinchcombe. 2008. Leaf variegation is associated with reduced herbivore damage in Hydrophyllum virginianum. Botany 86: 306-313.
[pdf] [Supplemental Figure S1]

Campitelli, B.E., A.K. Simonsen, A. Rico Wolf, J.S. Manson, and J.R. Stinchcombe. 2008. Leaf shape variation and herbivore consumption and performance: A case study with Ipomoea hederacea and three generalists. Arthropod-Plant Interactions 2: 9-19.
[pdf]

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2007

Simonsen, A.K. and J.R. Stinchcombe. 2007. Induced responses in Ipomoea hederacea: simulated mammalian herbivory induces resistance and susceptibility to insect herbivores. Arthropod-Plant Interactions. 1: 129-136 .
[pdf]

Johnson, M.T.J. and J.R. Stinchcombe. 2007. An emerging synthesis between community ecology and evolutionary biology. Trends in Ecology and Evolution 22: 250-257
[pdf]

Korves, T.M., K.J. Schmid, A.L. Caicedo, C. Mays, J.R. Stinchcombe, M.D. Purugganan, and J. Schmitt. 2007. Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. American Naturalist 169: E141-E157.
[pdf]

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2006

Stinchcombe, J.R. and J. Schmitt. 2006. Ecosystem engineers as selective agents: the effects of leaf litter on emergence time and early growth in Impatiens capensis. Ecology Letters 9: 258-270.
[pdf]

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2005

Stinchcombe, J.R., A.L. Caicedo, R. Hopkins, C. Mays, E.W. Boyd, M.D. Purugganan, and J. Schmitt. 2005. Vernalization sensitivity in Arabidopsis thaliana (Brassicaceae): the effects of latitude and FLC variation. American Journal of Botany 92: 1701-1707.
[pdf] [Supplemental Data] [Data on Dryad]

Stinchcombe, J.R. 2005. Measuring natural selection on proportional traits: comparisons of three types of selection estimates for resistance and susceptibility to herbivore damage. Evolutionary Ecology 18: 363-373.
[pdf]

Kelley, J.L., J.R. Stinchcombe, C. Weinig, and J. Schmitt. 2005. Hard and soft selection on plant defense traits in Arabidopsis thaliana. Evolutionary Ecology Research 7: 287-302 .
[pdf]

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2004

Caicedo, A.L., J.R. Stinchcombe, K.M. Olsen, J. Schmitt, M.D. Purugganan. 2004. Epistatic interaction between the Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. Proceedings of the National Academy of Sciences, USA 101: 15670-15675.
[pdf] [Supplemental Data]

Agrawal, A.A., J.K. Conner, and J.R. Stinchcombe. 2004. Evolution of plant resistance and tolerance to frost damage. Ecology Letters 7: 1199-1208.
[pdf]

Jackson, M.W., J.R. Stinchcombe*, T.M. Korves*, and J. Schmitt. 2004. Costs and benefits of cold tolerance in transgenic Arabidopsis thaliana. Molecular Ecology 13: 3609-3615.
(*) Authors contributed equally to this paper.
[pdf]

Agrawal, A.A., N. Underwood, and J.R. Stinchcombe. 2004. Intraspecific variation in the strength of density dependence in aphid populations. Ecological Entomology. 29: 521-526
[pdf]

Olsen, K.M., S.S. Halldorsdottir, J.R. Stinchcombe, C. Weinig, J. Schmitt, and M.D. Purugganan. 2004. Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167: 1361-1369.
[pdf] [Supplemental Data]

Stinchcombe, J.R., C. Weinig, M. Ungerer, K.M. Olsen, C. Mays, S.S. Halldorsdottir, M.D. Purugganan, and J. Schmitt. 2004. A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA. Proceedings of the National Academy of Sciences, USA 101: 4712-4717.
[pdf] [Supplemental Data] [Supplemental Figure]

Heschel, M.S.*, J.R. Stinchcombe*, K.E. Holsinger, and J. Schmitt. 2004. Natural selection on light response curve parameters in the herbaceous annual, Impatiens capensis. Oecologia 139: 487-494.
(*) Authors contributed equally to this paper.
[pdf]

Stinchcombe, J.R., L. Dorn, and J. Schmitt. 2004. Flowering time plasticity in Arabidopsis thaliana: A reanalysis of Westerman and Lawrence (1970). Journal of Evolutionary Biology 17: 197-207.
[pdf]

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2003

Schmitt, J., J.R. Stinchcombe, M.S. Heschel, H. Huber. 2003. The adaptive evolution of plasticity: phytochrome-mediated shade avoidance responses. Integrative and Comparative Biology 43: 459-469.
[pdf]

Moyle, L.C., J.R. Stinchcombe, B.R. Hudgens, and W.F. Morris. 2003. Conservation genetics in the recovery of endangered animal species: a review of U.S. endangered species recovery plans (1977-1998). Animal Biodiversity and Conservation 26: 85-95.
[pdf]

Weinig, C.*, J.R. Stinchcombe*, and J. Schmitt. 2003. Evolutionary genetics of resistance and tolerance to natural herbivory in Arabidopsis thaliana. Evolution 57: 1270-1280.
(*) Authors contributed equally to this paper.
[pdf]

Weinig, C., J.R. Stinchcombe, and J. Schmitt. 2003. QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments. Molecular Ecology 12: 1153-1163.
[pdf]

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2002

Stinchcombe, J.R., L.C. Moyle, B.R. Hudgens, P.L. Bloch, S. Chinnadurai, and W.F. Morris. 2002. The influence of the academic conservation biology literature on endangered species recovery planning. Conservation Ecology 6: 15. (Available on-line at: http://www.consecol.org/vol6/iss2/art15)
[pdf]

Stinchcombe, J.R. 2002. Can tolerance traits impose selection on herbivores? Evolutionary Ecology 16: 595-602.
[pdf]

Stinchcombe, J.R., M.T. Rutter, D.S. Burdick, P. Tiffin, M.D. Rausher, and R. Mauricio. 2002. Testing for environmentally induced bias in phenotypic estimates of natural selection: theory and practice. American Naturalist 160: 511-523.
[pdf] [Commentary by Kruuk, Merila, and Sheldon]

Stinchcombe, J.R. 2002. Environmental dependency in the expression of costs of tolerance to deer herbivory. Evolution 56: 1063-1067.
[pdf]

Stinchcombe, J.R. and M.D. Rausher. 2002. Evolution of tolerance to deer herbivory: modifications caused by the presence or absence of insects. Proceedings of the Royal Society of London, Ser. B 269: 1241-1246.
[pdf]

Morris, W.F., P.L. Bloch, B.R. Hudgens, L.C. Moyle, and J.R. Stinchcombe. 2002. The use of population viability analysis in endangered species recovery planning: past trends and recommendations for future improvement. Ecological Applications 12: 708-712.
[pdf] [Appendix A]

Stinchcombe, J.R. 2002. Fitness consequences of cotyledon and mature-leaf damage in the Ivyleaf morning glory. Oecologia 131: 220-226.
[pdf]

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2001

Stinchcombe, J.R. and M.D. Rausher. 2001. Diffuse selection on resistance to deer herbivory in the Ivyleaf Morning glory, Ipomoea hederacea. American Naturalist 158: 376-388.
[pdf]

Inouye, B. and J.R. Stinchcombe. 2001. Relationships between ecological interaction modifications and diffuse coevolution: similarities, differences, and causal links. Oikos 95: 353-360.
[pdf]

2000

Stinchcombe, J.R. 2000. U.S. Endangered species management: the influence of politics. Endangered Species Update 17: 118-121.
[pdf]

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