Publications

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Barker Lab members highlighted in bold

2017

54. Mandáková, T., Z. Li, M. S. Barker, and M. Lysak. 2017. Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention. The Plant Journal in press.

53. Kong, H., Y. Zhang, Y. Hong, and M. S. Barker. 2017. Multilocus phylogenetic reconstruction informing polyploid relationships of Aconitum subgenus Lycoctonum (Ranunculaceae) in China. Plant Systematics and Evolution in press.

52. Qi, X., H. An, A. Ragsdale, T. E. Hall, R. N. Gutenkunst, J. C. Pires, and M. S. Barker. 2017. Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Molecular Ecology in press.
Biorxiv Preprint

2016

51. The Pteridophyte Phylogeny Group. 2016. A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54(6): 563–603.
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50. Barker, M. S., B. C. Husband, and J. C. Pires. 2016. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. American Journal of Botany 103(7): 1139–1145. 
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49. Barker, M. S., Z. Li, T. I. Kidder, C. R. Reardon, Z. Lai, L. Oliveira, M. Scascitelli, and L. H. Rieseberg. 2016. Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae. American Journal of Botany 103(7): 1203–1211.
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48. Baniaga, A. E., N. Arrigo, and M. S. Barker. 2016. The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution. Genome Biology and Evolution 8: 1516–1525.
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47. Arrigo, N., M. de La Harpe, G. Litsios, J. Zozomova-Lihova, S. Spaniel, K. Marhold, M. S. Barker, and N. Alvarez. 2016. Is hybridization driving the evolution of climatic niche in Alyssum montanum (Brassicaceae)? American Journal of Botany 103(7): 1348–1357. 
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46. Barker, M. S., N. Arrigo, A. E. Baniaga, Z. Li, and D. A. Levin. 2016. On the relative abundance of autopolyploids and allopolyploids. New Phytologist 210: 391–398.
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45. Marques, I, S. Montgomery, M. S. Barker, T. Macfarlane, J. Conran, P. Catalan, L. H. Rieseberg, P. J. Rudall, and S. W. Graham. 2016. Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). New Phytologist 210: 310–323. 
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2015

44. Li, Z., A. E. Baniaga, E. B. Sessa, M. Scascitelli, S. W. Graham, L. H. Rieseberg, and M. S. Barker. 2015. Early genome duplications in conifers and other seed plants. Science Advances 1(10): e1501084. 
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43. Edger, P. E., H. M. Heidel-Fischer, M. Bekaert, J. Rota, G. Glockner, A. E. Platts, D. Heckel, J. P. Der, E. K. Wafula, M. Tang, J. A. Hofberger, A. Smithson, J. C. Hall, M. Blanchette, T. E. Bureau, S. I. Wright, C. W. dePamphilis, M. E. Schranz, M. S. Barker, G. C. Conant, N. Wahlberg, H. Vogel, J. C. Pires, and C. W. Wheat. 2015. The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences of the USA 112(27): 8362–8366. 
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42. Mayrose, I., S. H. Zhan, C. J. Rothfels, N. Arrigo, M. S. Barker, L. H. Rieseberg, and S. P. Otto. 2015. Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014). New Phytologist 206(1): 27–35. 
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2014

41. Wickett, N. J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam,M. S. Barker, G. J. Burleigh, M. A. Gitzendanner, B. Ruhfel, E. Wafula, J. Der, S. W. Graham, S. Mathews, M. Melkonian, D. E. Soltis, P. S. Soltis, C. Rothfels, L. Pokorny, J. Shaw, L. DeGeronimo, D. Stevenson, B. Surek, J. C. Villareal, B. Roure, H. Philippe, C. W. dePamphilis, T. Chen, M. Deyholos, J. Wang, Y. Zhang, Z. Tian, Z. Yan, X. Wu, X. Sun, G. K.-S. Wang, J. Leebens-Mack. A phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the USA111(45): E4859–4868. 
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40. Matasci, N., L.-H. Hung, Z. Yan, E. J. Carpenter, N. J. Wickett, S. Mirarab, N. Nguyen, T. Warnow, S. Ayyampalayam, M. S. Barker, J. G. Burleigh, M. A. Gitzendanner, E. Wafula, J. P. Der, C. W. dePamphilis, B. Roure, H. Philippe, B. R. Ruhfel, N. W. Miles, S. W. Graham, S. Mathews, B. Surek, M. Melkonian, D. E. Soltis, P. S. Soltis, C. Rothfels, L. Pokorny, J. A. Shaw, L. DeGironimo, D. W. Stevenson, J. C. Villareal, T. Chen, T. M. Kutchan, M. Rolf, R. S. Baucom, M. K. Deyholos, R. Samudrala, Z. Tian, X. Wu, X. Sun, Y. Zhang, J. Wang, J. Leebens-Mack, and G. K.-S. Wong. 2014. Data access for the 1000 Plants (1KP) pilot.GigaScience 3: 17. 
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39. Sessa, E.B., J. A. Banks, M. S. Barker, J. P. Der, A. M. Duffy, S. W. Graham, M. Hasebe, J. Langdale, F-W Li, D. B. Marchant, K. M. Pryer, C. J. Rothfels, S. J. Roux, M. L. Salmi, D. E. Soltis, P. S. Soltis, D. W. Stevenson, and P. G. Wolf. 2014. Between two fern genomes.GigaScience 3(1): 15. 
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2013

38. Hodgins, K. A., Z. Lai, L. O. Oliveira, D. W. Still, M. Scascitelli, M. S. Barker, N. C. Kane, H. Dempewolf, A. Kozik, R. V. Kesseli, J. M. Burke, R. W. Michelmore, and L. H. Rieseberg. 2013. Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Molecular Ecology Resources 14(1): 166–177. 
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37. Arrigo, N., J. Therrien, C. L. Anderson, M. D. Windham, C. H. Haufler, and M. S. Barker. 2013. A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys. American Journal of Botany 100(8): 1672–1682. 
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2012

36. Bowers, J. E., S. Nambeesan, J. Corbi, M. S. Barker, L. H. Rieseberg, S. J. Knapp, and J. M. Burke. 2012. Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms. PLoS One 7(12): e51360. 
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35. Barker, M. S. 2012. Karyotype and genome evolution in Pteridophytes. Pp. 245–253 in Plant Genome Diversity, Volume 2, I. J. Leitch, ed. Springer, Vienna. 
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34. Arrigo, N., L. P. Albert, P. G. Mickelson, and M. S. Barker. 2012. Quantitative visualization of biological data in Google Earth using R2G2, an R CRAN package. Molecular Ecology Resources 12: 1177–1179. 
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33. Arrigo, N. and M. S. Barker. 2012. Rarely successful polyploids and their legacy in plant genomes. Current Opinion in Plant Biology 15: 140–146. 
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32. Barker, M. S., G. J. Baute, and S.-L. Liu. 2012. Duplications and turnover in plant genomes, Volume 1. Pp. 155–169 in Plant Genome Diversity, J. F. Wendel, ed. Springer, Vienna. 
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31. Zhao, L., N. C. Kane, A. Kozik, K. A. Hodgins, K. M. Dlugosch, M. S. Barker, M. Matvienko, Q. Yu, K. G. Turner, S. A. Pearl, G. D. M. Bell, Y. Zou, C. Grassa, A. Guggisberg, K. L. Adams, J. V. Anderson, D. P. Horvath, R. V. Kesseli, J. M. Burke, R. W. Michelmore, and L. H. Rieseberg. 2012. Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. American Journal of Botany 99: 209–218. 
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2011

30. Mayrose, I., S. H. Zhan, C. J. Rothfels, K. Magnuson-Ford, M. S. Barker, L. H. Rieseberg, and S. P. Otto. 2011. Recently-formed polyploid plants diversify at lower rates. Science 333: 1257.
PDF Data UA News F1000 Brandvain’s Blog

29. Kane, N. C., M. S. Barker, S. H. Zhan, and L. H. Rieseberg. 2011. Molecular evolution across the Asteraceae: micro- and macroevolutionary processes. Molecular Biology and Evolution28: 3225–3235. 
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28. Banks, J. A., T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. DePamphilis, V. A. Albert, N. Aono, T. Aoyama, B. A. Ambrose, N. W. Ashton, M. J. Axtell, E. Barker, M. S. Barker, et al. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332: 960–963. 
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27. Der, J. P., M. S. Barker, N. J. Wickett, C. W. DePamphilis, and P. G. Wolf. 2011. De novocharacterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 12: 99. 
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2010

26. Barker, M. S., K. M. Dlugosch, L. Dinh, R. S. Challa, N. C. Kane, M. G. King, and L. H. Rieseberg. 2010. EvoPipes.net: Bioinformatic tools for ecological and evolutionary genomics.Evolutionary Bioinformatics 6: 143–149. 
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25. Shi, T., H. Huang, and M. S. Barker. 2010. Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Annals of Botany 106: 497–504. 
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24. Dlugosch, K. M., M. S. Barker, and L. H. Rieseberg. 2010. NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform. BMC Research Notes 3: 217. 
PDF Software Download

23. Dempewolf, H., N. C. Kane, K. L. Ostevik, M. Geleta, M. S. Barker, Z. Lai, M. L. Stewart, E. Bekele, J. M. M. Engels, Q. C. B. Cronk, and L. H. Rieseberg. 2010. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass. — the development of a library of expressed sequence tags, microsatellite loci and the sequencing of its chloroplast genome.Molecular Ecology Resources 10: 1048–1058. 
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22. Barker, M. S. and P. G. Wolf. 2010. Unfurling fern biology in the genomics age. BioScience60(3): 177–185. 
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21. Mayrose, I., M. S. Barker, and S. P. Otto. 2010. Probabilistic models of chromosome number evolution and the inference of polyploidy. Systematic Biology 59(2): 132–144. 
PDF chromEvol Software Download

2009

20. Barker, M. S., H. Vogel, and M. E. Schranz. 2009. Paleopolyploidy in the Brassicales: Analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales. Genome Biology and Evolution 1(1): 391–399. 
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19. Barker, M. S. and G. Yatskievych. 2009. Summary of the 2008 AFS Symposium: From gels to genomics: The evolving landscape of pteridology. A celebration of Gerald Gastony’s Contributions to Fern Evolutionary Biology. American Fern Journal 99(2): 117–141. 
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18. Wood, T. E., N. Takebayashi, M. S. Barker, I. Mayrose, P. B. Greenspoon, and L. H. Rieseberg. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences USA 106(33): 13875–13879. 
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17. Kane, N. C., M. King, M. S. Barker, A. Raduski, S. Karrenberg, Y. Yatabe, S. J. Knapp, and L. H. Rieseberg. 2009. Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent Helianthus species.Evolution 63(8): 2061–2075.
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16. Barker, M. S.*, K. M. Dlugosch*, A. C. C. Reddy, S. N. Amyotte, and L. H. Rieseberg. 2009. SCARF: Maximizing next-generation EST assemblies for evolutionary and population genomic analyses. Bioinformatics 25(4): 535–536. 
PDF *Co-first authors SCARF Downloads Bioinformatics Next Gen Sequencing Virtual Issue

2008

15. Barker, M. S., N. C. Kane, M. Matvienko, A. Kozik, R. W. Michelmore, S. J. Knapp, and L. H. Rieseberg. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 25(11): 2445–2455. 
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14. Nakazato, T., M. S. Barker, L. H. Rieseberg, and G. J. Gastony. 2008. Evolution of the nuclear genome of ferns and lycophytes. Pp. 177–200 in:The Biology and Evolution of Ferns and Lycophytes, T. Ranker and C. Haufler, eds. Cambridge University Press.

13. Shaw, S. W., S. V. Sprunt, and M. S. Barker. 2008. New records for Puerto Rican Ferns.American Fern Journal 98(2): 107–111.
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2007 & Earlier

12. Brandvain, Y.*, M. S. Barker*, and M. J. Wade. 2007. Gene co-inheritance and gene transfer.Science 315: 1685. 
PDF *Co-first authors IU Press Release

11. Barker, M. S. and R. J. Hickey. 2006. A revision of Caribbean Adiantopsis (Pteridaceae). Annals of the Missouri Botanical Garden 93(3): 371–401. 
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10. Barker, M. S. and L. Sanchez. 2005. Inks Lake State Park and Westcave Preserve, Botany 2005 AFS Fern Foray. Fiddlehead Forum: Bulletin of the American Fern Society 32(4–5): 31–33.

9. Barker, M. S., J. P. Demuth, and M. J. Wade. 2005. Maternal expression relaxes constraint on innovation of the anterior determinant, bicoid. PLoS Genetics 1(5): e57.* 
PDF Nature Reviews Genetics Highlight

8. Barker, M. S., S. W. Shaw, R. J. Hickey, J. E. Rawlins, and J. Fetzner. 2005. Lepidopteran soral crypsis on Caribbean ferns. Biotropica 37(2): 314–316. * 
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7. Barker, M. S. 2005. A Natural History of Ferns by Robbin C. Moran. American Fern Journal95(3): 128–129. 
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6. Shaw, S. W., M. S. Barker, and R. J. Hickey. 2004. New municipality records for Puerto Rican pteridophytes. Fern Gazette 17: 97–99. 
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5. Hauk, W. D. and M. S. Barker. 2003. Botrychium lanceolatum subsp. angustisegmentum in Ohio.American Fern Journal 93(2): 93–94. 
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4. Hickey, R. J., M. S. Barker, and M. Ponce. 2003. An Adiantopsis hybrid from northeastern Argentina and vicinity. American Fern Journal 93(1): 42–44. 
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3. Barker, M. S. and W. D. Hauk. 2003. An evaluation of Sceptridium dissectum (Ophioglossaceae) with ISSR markers: Implications for Sceptridium systematics. American Fern Journal 93(1): 1–19. 
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2. Hauk, W. D. and M. S. Barker. 2000. Larch Mountain, 2000 AFS Fern Foray. Fiddlehead Forum: Bulletin of the American Fern Society. 27(5): 26–27.

1. Barker, M. S. 1999. A molecular assessment of infraspecific genetic variation in Draba verna L. using ISSR (Inter-Simple Sequence Repeat) Markers. Denison Journal of Biological Science. 33(1): 27–34.