Publications

Zagori mountains

Zagori mountains, home of Capsella grandiflora
Photo by John Paul Foxe

See Google Scholar listing:  Stephen I. Wright               

* contributed equally, ** corresponding authors and/or co-supervision

2016

Josephs, E., Stinchcombe, J.R.*, and Wright, S.I.*. What can genome-wide association studies tell us about the evolutionary forces maintaining variation for quantitative traits? New Phytologist. In press (Tansley Review).

Arunkumar, R. Maddison, T., Barrett, S.C.H., and Wright, S.I. in press. Recent mating system evolution in Eichhornia is accompanied by cis-regulatory divergence. New Phytologist.

Brandvain, Y. and Wright, S.I. 2016. The limits of natural selection in a non-equilibrium world. Trends in Ecol. Evol. 32(4):201-10.

Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright, SI, Lagercrantz U, and Lascoux M. 2016. The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae). Mol. Ecol. 25(5):1106-21.

Hartfield M, Wright SI, and Agrawal AF.2016. Coalescent times and patterns of genetic diversity in species with facultative sex: effects of gene conversion, population structure, and heterogeneity. Genetics. 202(1):297-312.

Cornille A, Salcedo A , Kryvokhyzha D, Glémin S, Holm K, Wright, SI, and Lascoux, M. 2016. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa-pastoris). Mol Ecol. 25(2):616-29.

2015

Josephs, E., Lee, Y.W., Stinchcombe, J.R., & Wright, S.I. (2015). Association mapping reveals the role of mutation-selection balance in the maintenance of genomic variation for gene expression. PNAS 112: 15390–15395 doi: http://dx.doi.org/10.1101/015743

Ågren, J.A., & Wright, S.I. (2015). Selfish genetic elements and plant genome size evolution. Trends Plant Sci., 20(4): 195-196http://dx.doi.org/10.1016/j.tplants.2015.03.007

Douglas, G.M.*, Gos, G.*, Steige, K.A.*, Salcedo, A., Holm, K., Josephs, E.B., Arunkumar, R., Ågren, J.A., Hazzouri, K.M., Wang, W., Platts, A.E., Williamson, R.J., Neuffer, B., Lascoux, M.**, Slotte, T.**, Wright, S.I.**. (2015). Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploidy Capsella bursa-pastoris. Proceedings of the National Academy of Sciences, USA 112(9):  2806–2811, doi: 10.1073/pnas.1412277112

Ågren, J.A., Greiner S., Johnson M.T.J., Wright S.I. (2015). No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution 69(4): 1053-1062, doi: 10.1111/evo.12627

Hollister J.D., Greiner S., Wang W., Wang J., Zhang Y., Wong G.K., Wright S.I.**, and Johnson M.T.**. (2015). Recurrent loss of sex is associated with accumulation of deleterious mutations in Oenothera. Molecular Biology and Evolution. 32(4): 896-905,  doi: 10.1093/molbev/msu345

2014

Arunkumar, R., Ness R.W., Wright S.I., Barrett S.C.H. (2014). The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations. Genetics 199(3): 817-829, doi: 10.1534/genetics.114.172809

Ågren J.A. , Wang W. , Koenig D. , Neuffer B., Weigel D., Wright S.I., (2014). Mating system shifts and transposable element evolution in the plant genus Capsella., BMC Genomics, 15(1): 602

Huang Y., Wright S.I., Agrawal A.F. (2014). Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes. PloS Genetics, 10(8): e1004527

Sicard, A., Thamm, A., Marona C., Lee Y.W., Wahl V. , Stinchcombe J.R., Wright S.I., Kappel C., Lenhard M. (2014). Repeated evolutionary changes of leaf morphology caused by mutations to a homeobox gene. Current Biology, 24(16): 1880-1886

Barrett S.C.H., Arunkumar R., & Wright S.I. (2014). The demography and population genomics of evolutionary transitions to self-fertilization in plants. Philosophical Transactions of the Royal Society of London Ser. B.  369:  20130344.  http://dx.doi.org/10.1098/rstb.2013.0344

Hough J., Hollister J.D., Wang W., Barrett S.C.H., & Wright S.I. (2014). Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus. Proceedings of the National Academy of Sciences USA, 111(21): 7713-8  doi:10.1073/pnas.1319227111

Salcedo, A., Kalisz, S., & Wright, S.I. (2014). Limited genomic consequences of mixed mating in the recently derived sister species pair, Collinsia concolor and Collinsia parryiJournal of evolutionary biology. 27: 1400-1412. DOI: 10.1111/jeb.12384

Williamson, R.*, Josephs, E.B.*, Platts, A. E., Hazzouri, K.M., Haudry, A., Blanchette, M., & Wright, S.I. (2014).  Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora. PloS Genetics 10: e1004622.  joint first authors

Wright, S.I. (2014).   Mutationism 2.0: Viewing evolution through mutation’s lens.  Evolution, 68: 1225–1227. doi: 10.1111/evo.12369

 

2013

Hough, J., Williamson, R.J., & Wright, S.I. (2013). Patterns of selection in plant genomes. Annual Review of Ecology, Evolution, and Systematics44: 31-49.

Arunkumar, R., Josephs, E.B., Williamson, R.J., & Wright, S.I. (2013). Pollen-Specific, but Not Sperm-Specific, Genes Show Stronger Purifying Selection and Higher Rates of Positive Selection Than Sporophytic Genes in Capsella grandifloraMolecular Biology and Evolution30: 2475-2486.

Brandvain, Y.  Slotte T., Hazzouri K.M., Wright S.I., Coop G. (2013).  Genomic Identification of founding haplotypes reveals the history of the selfing species Capsella rubellaPLoS Genet. 2013 Sep;9(9):e1003754.

Haudry, A., Platts, A.E., Vello, E., Hoen, D.R., Leclercq, M., Williamson, R.J., Forczek, E., Joly-Lopez, Z., Steffen, J.G., Hazzouri, K.M., Dewar, K., Stinchcombe, J.R., Schoen, D.J., Wang, X., Schmutz, J., Town, C.D., Edger, P.P., Pires, J.C., Schumaker, K.S., Jarvis, D.E., Mandáková, T., Lysak, M.A., van den Bergh, E., Schranz, M.E., Harrison, P.M., Moses, A.M.**, Bureau, T.E.**, Wright, S.I.** & Blanchette, M.**. (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 (see links to paper in EEB News)

Slotte, T., Hazzouri, K.M., Ågren, J.A, Koenig, D., Maumus, F., Guo, Y.L., Steige, K., Platts, A.E., Escobar, J.S., Newman, L.K., Wang W., Mandáková, T., Vello, E., Smith, L.M., Henz, S.R., Steffen, J., Takuno, S., Brandvain,Y., Coop, G., Andolfatto, P., Hu, T.T., Blanchette, M., Clark, R.M., Quesneville, H., Nordborg, M., Gaut, B.S., Lysak, M.A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D.** & Wright, S.I.**(2013).  The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics 45(7): 831–835(2013) doi:10.1038/ng.2669

Wright, S.I., Kalisz, S., Slotte, T. (2013).  Evolutionary consequences of self-fertilization in plants.  Proc. R. Soc. B 280(1760):  doi: 10.1098/rspb.2013.0133

Hazzouri, K.M.*, Escobar, J.*, Ness, R.W.*, Newman, L.K., Randle, A., Kalisz, S., and Wright, S.I. (2013).  Comparative population genomics in Collinsia sister species reveals evidence for reduced effective population size, relaxed selection and evolution of biased gene conversion with an ongoing mating system shift. Evolution 67(5): 1263-1278. DOI: 10.1111/evo.12027 (*, first authors)

2012

Indriolo, E., Tharmapalan, P., Wright, S.I. and Goring, D.R. (2012).  The ARC1 E3 ligase gene is frequently deleted in self-compatible Brassicaceae species and has a conserved role in Arabidopsis lyrata self-pollen rejection. Plant Cell 24(11): 4607-4620. DOI: 10.1105/tpc.112.104943

Slotte T., Hazzouri K.M.*, Stern D., Andolfatto P., and Wright, S.I. (2012).  Genetic architecture and adaptive significance of the selfing syndrome in Capsella.Evolution 66(5):1360-1374. (*, first authors)

St. Onge K.*, Foxe, J.P.*, Junrui, L., Haipeng, L., Holm, K., Corcoran, P.,Slotte, T.  Lascoux, M.** and Wright, S.I.** (2012).  Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd’s purse (Capsella bursa-pastoris). Mol. Biol. Evol. 29(7): 1721-33.

St. Onge, K., Palmé A.E., Wright, S.I. and Lascoux, M. The impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories. G3 2(7): 803-14.

 

2011
Slotte T.*, Bataillon T.*, Hansen T.T., St Onge K., Wright S.I., Schierup M.H. (2011). Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol. Evol. 3: 1210-1219.
* joint first authors

Ågren J.A., Wright S.I. (2011).  Co-evolution between transposable elements and their hosts: a major factor in genome size evolution? Chromosome Research 19: 777-786.

Wright S.I., Ågren J.A. (2011). The Arabidopsis lyrata genome sequence. Sizing up Arabidopsis genome evolution. Heredity 107(6): 509-510. DOI: 10.1038/hdy.2011.47

Roux C, Castric V, Pauwels M, Wright SI, Saumitou-Laprade P, Vekemans X. (2011).  Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation? PloS One6:e26872.

Qiu S.*, Zeng K.*, Slotte T.*, Wright S. I., Charlesworth D. (2011). Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species.Genome Biol Evol. 868-880.
* joint first authors

 

2010
Wright, S.I. and S.C.H. Barrett. (2010).  The long-term benefits of self-rejection.Science 330: 459-460. (Perspectives)

Charlesworth D., Qiu S., Bergero R., Ågren J.A., and S.I. Wright. (2010).  Using DNA sequence diversity to test for selection in SileneInternational Journal of Plant Sciences. 171:1072-1082.

Siol M., Wright S.I., and S.C. Barrett. (2010).  The population genomics of plant adaptation. New Phytologist. 188: 313-332.

Foxe J.P., Stift M., Tedder A., Haudry A., Wright S.I., and B.K. Mable. (2010).  Reconstructing origins of loss of self-incompatibility and selfing in North AmericanArabidopsis lyrata: A population genetic context. Evolution. 64: 3495-3510.

Slotte T., Foxe J.P., Hazzouri K.M., and S.I. Wright. (2010).  Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Molecular Biology and Evolution 27: 1813-1821.

Evans B.J., Pin L., Melnick D.J., and S.I. Wright. (2010).  Sex-linked inheritance in macaque monkeys: Implications for effective population size and dispersal to Sulawesi. Genetics. 185: 923-937.

Ness, R.W., Wright, S.I., and Barrett, S.C.H. (2010).  Mating system variation, demographic history and patterns of nucleotide diversity in the tristylous plant Eichhornia paniculata. Genetics 184: 381-392.

 

2009
Foxe, J.P. and Wright, S.I. (2009).  Signature of diversifying selection on members of the pentatricopeptide repeat protein family. Genetics. 183: 663-672.

Foxe, J.P.*, Slotte, T.*, Stahl, E., Neuffer, B., Hurka, H., and Wright, S.I. (2009).  Recent speciation associated with the evolution of selfing in Capsella. Proceedings of the National Academy of Sciences USA 106(13): 5241-5. *, joint first authors.

Morton, B., Dar, N., and Wright, S.I. (2009).  Analysis of site frequency spectra from Arabidopsis thaliana with context-dependent corrections for ancestral misinference. Plant Physiology 149: 616-624.

Bagherie-Lachidan, M., Wright, S.I., and Kelly, S.P. (2009).  Claudin-8 and -27 tight junction proteins in puffer fish Tetraodon nigroviridis acclimated to freshwater and seawater. Journal of Comparative Physiology B 179: 419-431.

 

2008
Gos, G. and Wright, S.I. (2008).  Conditional neutrality at two adjacent NBS-LRR disease resistance loci in natural populations of Arabidopsis lyrata. Molecular Ecology 17: 4953-4962.

Kawabe, A., Forrest, A., Wright, S.I. and Charlesworth, D. (2008).  High DNA sequence diversity in pericentromeric genes in Arabidopsis lyrata. Genetics 179: 985-995.

Ross-Ibarra, J.*, Wright, S.I.*, Foxe, J.P., Kawabe, A., DeRose Wilson, L., Gos, G., Charlesworth, D., and Gaut, B.S. (2008).  Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PloS One3:e2411.
* joint first authors.

Foxe, J.P., Dar, N., Zheng, H., Nordborg, M., Gaut, B.S., and Wright, S.I. (2008).  Selection on amino acid substitutions in Arabidopsis. Molecular Biology and Evolution 25: 1375-1383.

Hazzouri, K.M., Mohajer, A., Dejak, S.I., Otto, S.P., and Wright, S.I. (2008).  Contrasting patterns of transposable element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species.Genetics 179: 581-592.

Bagherie-Lachidan, M., Wright, S.I. and Kelly, S.P. (2008).  Claudin-3 tight junction proteins in Tetraodon nigroviridis: Cloning, tissue specific expression and a role in hydromineral balance. American Journal of Physiology-Regulatory, Integrative, and Comparative 294: R1638-1647.

Wright, S.I. and Andolfatto, P. (2008).  The impact of natural selection on the genome: emerging patterns from Drosophila and Arabidopsis. Annual Review of Ecology Evolution and Systematics 39: 193-213.

Wright, S.I., Nano, N., Foxe, J.P., and Dar,N. (2008).  Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis. Genetics Research 90: 119-128.

Wright, S.I., Ness, R.W., Foxe, J.P., and Barrett, S.C.H. (2008).  Genomic consequences of selfing and outcrossing in plants. International Journal of Plant Sciences 169: 105-118.

 

2007
Yamasaki, M., Wright, S.I., and McMullen, M.D. (2007).  Genomic screening for artificial selection during domestication and improvement in maize. Annals of Botany. 100: 967-973.

Gaut, B.S., Wright, S.I., Rizzon, C., Dvorak, J. and Anderson, L. (2007).  Recombination: an underappreciated factor in the evolution of plant genomes. Nature Reviews Genetics 8: 77-84.

Wright, S.I., Iorgovan, G., Misra, M. and Mokhtari, M. (2007).  Neutral evolution of synonymous base composition in the Brassicaceae. Journal of Molecular Evolution 64: 136-141.

Morton, B. and Wright, S.I. (2007).  Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana. Molecular Biology and Evolution 24: 122-129.

 

2004 – 2006
Wright, S.I., Foxe, J.P., DeRose Wilson, L., Kawabe, A., Looseley, M., Gaut, B., and Charlesworth, D. (2006).  Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata. Genetics 174: 1421-1430.

Wright, S.I., Bi I.V., Schroeder S.G., Yamasaki, M., Doebley, J.F., McMullen, M.D., and Gaut, B.S. (2005).  The effects of artificial selection on the maize genome. Science 308: 1310-1314.

International Rice Genome Sequencing Project (2005).  The map-based sequence of the rice genome. Nature 436: 793-800.

Wright, S.I. and Gaut, B.S. (2005).  Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution 22: 506-519.

Wright, S.I. and Charlesworth, B. (2004).  The HKA test revisited: A maximum likelihood ratio test of the standard neutral model. Genetics 168: 1071-1076.

Marais, G., Charlesworth B.and Wright, S.I. (2004). Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biology 5: R45.

Wright, S.I., Yau, C.B.K., Looseley, M. and B. Meyers. (2004). Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Molecular Biology and Evolution 21: 1719-1726.

 

1999-2003

Wright, S.I., Agrawal, N. and Bureau, T.E. (2003).   Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Research 13: 1897-1903.

Wright, S.I., Lauga, B. and Charlesworth, D. (2002).  Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. Molecular Biology and Evolution 19: 1399-1406.

Charlesworth, D. and Wright, S.I. (2001).  Breeding systems and genome evolution. Current Opinion in Genetics and Development 11: 685-690.

Wright, S.I. and Finnegan, D. (2001).  Genome Evolution: Sex and the transposable element. Current Biology 11: R296-R299.

Wright, S.I., Le, Q.H., Schoen, D.J., and Bureau, T.E. (2001).  Population dynamics of an Ac-like transposable element in self- and cross-pollinating Arabidopsis. Genetics 158: 1279-1288.

Yu, Z., Wright, S.I., and Bureau, T.E. (2000).  Mutator-like elements in Arabidopsis thaliana: structure, diversity and evolution. Genetics 156: 2019-2031.

Le Q.H.*, Wright, S.I.*, Yu, Z. and Bureau, T.E. (2000).   Transposon diversity in Arabidopsis thaliana. Proceedings of the National Academy of Sciences USA 97: 7376-7381. *-joint first authorship.

Wright, S.I. and Schoen D.J. (1999).   Transposon dynamics and the breeding system. Genetia 107: 139-148.

Wright, S.I. and Barrett, S.C.H. (1999).  Size-dependent gender modification in a hermaphroditic perennial herb. Proceedings of the Royal Society of London B 266: 225-232.