Source: https://www.barkerlab.net/publications
Timestamp: 2019-04-20 11:00:55+00:00

Document:
Baniaga, A. E., H. E. Marx, N. Arrigo, and M. S. Barker. Polyploid plants have faster rates of multivariate niche evolution than their diploid relatives. bioRxiv https://doi.org/10.1101/406314.
Baniaga, A. E. and M. S. Barker. Nuclear genome size is positively correlated with mean LTR insertion date in fern and lycophyte genomes. bioRxiv https://doi.org/10.1101/571570.
An, H., X. Qi, M. Gaynor, Y. Hao, S. Gebken, M. Mabry, G. C. Conant, M. S. Barker, T. Fu, B. Yi, and J. C. Pires. Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. In review.
One Thousand Plant Transcriptomes Initiative. A Phylogenomic View of Evolutionary Complexity in Green Plants. In review.
63. Wong, G. K.-S., D. E. Soltis, J. Leebens-Mack, N. J. Wickett, M. S. Barker, Y. Van de Peer, S. W. Graham, and M. Melkonian. 2019. Sequencing and analyzing the transcriptomes of a thousand plant species across the tree of life for green plants. Annual Review of Plant Biology in press.
62. Li, Z., G. P. Tiley, R. J. Rundell, and M. S. Barker. 2019. Reply to Nakatani and McLysaght: Analyzing deep duplication events. Proceedings of the National Academy of Sciences of the USA 116: 1819–1820.
61. Tiley, G. P., M. S. Barker, and J. G. Burleigh. 2018. Assessing the performance of Ks plots for detecting ancient whole genome duplications. Genome Biology and Evolution 10: 2882–2898.
60. Li, F.-W., P. Brouwer, L. Carretero-Paulet, S. Cheng, J. de Vries, P.-M. Delaux, A. Eily, N. Koppers, L.-Y. Kuo, Z. Li, M. Simenc, I. Small, E. Wafula, S. Angarita, M. S. Barker, A. Brautigam, C. dePamphilis, S. Gould, P. S. Hosmani, Y.-M. Huang, B. Huettel, Y. Kato, X. Liu, S. Maere, R. McDowell, L. A. Mueller, K. G. J. Nierop, S. A. Rensing, T. Robison, C. J. Rothfels, E. M. Siegel, Y. Song, P. R. Timilsena, Y. Van de Peer, H. Wang, P. K. I. Wilhelmsson, P. G. Wolf, X. Xu, J. P. Der, H. Schluepmann, G. K.-S. Wong, and K. M. Pryer. 2018. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants 4: 460–472.
59. Landis, J.B., D. S. Soltis, Z. Li, H. E. Marx, M. S. Barker, D. C. Tank, and P. S. Soltis. 2018. Impact of whole-genome duplication events on diversification rates in angiosperms. American Journal of Botany 105(3): 348–363.
58. Li, Z., G. Tiley, S. Galuska*, C. Reardon*, T. Kidder*, R. Rundell, and M. S. Barker. 2018. Multiple large-scale gene and genome duplications during the evolution of hexapods. Proceedings of the National Academy of Sciences of the USA 115: 4713–4718.
57. Barker, M. S. 2018. A Gneato nuclear genome. Nature Plantsdoi:10.1038/s41477–018–0102–4.
56. Mandel, J. R., M. S. Barker, R. J. Bayer, R. B. Dikow, T. Gao, K. E. Jones, S. Keeley, N. Kilian, H. Ma, C. M. Siniscalchi, A. Susanna, R. Thapa, L. Watson, and V. A. Funk. 2017. The Compositae Tree of Life in the age of phylogenomics. Journal of Systematics and Evolution 55: 405–410.
55. Yu, R., A. E. Baniaga, S. A. Jorgensen, and M. S. Barker. 2017. A successful in vitro propagation technique for resurrection plants of the Selaginellaceae. American Fern Journal 107: 96–104.
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 91: 3–21.
53. Kong, H., Y. Zhang, Y. Hong, and M. S. Barker. 2017. Multilocus phylogenetic reconstruction informing polyploid relationships of Aconitumsubgenus Lycoctonum (Ranunculaceae) in China. Plant Systematics and Evolution 303: 727–744.
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 26: 3373–3388.
51. The Pteridophyte Phylogeny Group. 2016. A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54(6): 563–603.
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.
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.
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.
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.
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 Phytologist210: 391–398.
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.
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.
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.
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.
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.
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.
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.
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.
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.
36. Barker, M. S. 2013. Karyotype and genome evolution in Pteridophytes. Pp. 245–253 in Plant Genome Diversity, Volume 2, I. J. Leitch, ed. Springer, Vienna.
35. 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 One7(12): e51360.
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.
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.
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.
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.
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.
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 Evolution 28: 3225–3235.
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.
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.
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.
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.
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.
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.
22. Barker, M. S. and P. G. Wolf. 2010. Unfurling fern biology in the genomics age. BioScience 60(3): 177–185.
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.
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.
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.
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.
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.
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.
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.
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.
12. Brandvain, Y.^, M. S. Barker^, and M. J. Wade. 2007. Gene co-inheritance and gene transfer. Science 315: 1685.
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.
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.
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.
7. Barker, M. S. 2005. A Natural History of Ferns by Robbin C. Moran. American Fern Journal 95(3): 128–129.
6. Shaw, S. W., M. S. Barker, and R. J. Hickey. 2004. New municipality records for Puerto Rican pteridophytes. Fern Gazette 17: 97–99.
5. Hauk, W. D. and M. S. Barker*. 2003. Botrychium lanceolatum subsp. angustisegmentum in Ohio. American Fern Journal 93(2): 93–94.
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.
3. Barker, M. S.* and W. D. Hauk. 2003. An evaluation of Sceptridium dissectum (Ophioglossaceae) with ISSR markers: Implications for Sceptridiumsystematics. American Fern Journal 93(1): 1–19.
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.

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