Publications

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Preprints

McKibben, M. T. W. and M. S. Barker. Applying machine learning to classify the origins of gene duplications. bioRxiv preprint: https://doi.org/10.1101/2021.08.12.456144
Frackify Repository: https://gitlab.com/barker-lab/frackify

Wickell, D., L.-Y. Kuo, H.-P. Yang, A. D. Ashok, I. Isarri, A. Dadras, S. de Vries, J. de Vries, Y.-M. Huang, Z. Li, M. S. Barker, N. T. Hartwick, T. P. Michael, and F.-W. Li. Underwater CAM photosynthesis elucidated by Isoetes genome. bioRxiv preprint: https://doi.org/10.1101/2021.06.09.447806.

Heckenhauer, J., P. B. Frandsen, J. S. Sproul, Z. Li, J. Paule, A. M. Larracuente, P. J. Maughan, M. S. Barker, J. V. Schneider, and S. U. Pauls. Genome size evolution in the diverse insect order Trichoptera.
bioRxiv preprint: https://doi.org/10.1101/2021.05.10.443368

Zhan, S. H., S. P. Otto, and M. S. Barker. Broad variation in the rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification.
bioRxiv preprint: https://doi.org/10.1101/2021.03.30.436382

2021

Bayer, P., A. Scheben, A. Golicz, Y. Yuan, S. Faure, H. T. Lee, H. Chawla, R. Anderson, I. Bancroft, H. Raman, Y. P. Lim, S. Robbens,L. Jiang, S. Liu, M. S. Barker, E. Schranz, X. Wang, G. King, J. C. Pires, B. Chalhoub, R. Snowdon, J. Batley, and D. Edwards. 2021. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. Plant Biotechnology Journal in press.

Román-Palacios, C., C. A. Medina, S. H. Zhan, and M. S. Barker. 2021. Animal chromosome counts reveal a similar range of chromosome numbers but with less polyploidy in animals compared to plants. Journal of Evolutionary Biology in press.
bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2020.10.10.334722v1
DOI: https://doi.org/10.1111/jeb.13884
Animal Chromosome Count Database: https://cromanpa94.github.io/ACC/

Li, Z., M. T. W. McKibben, G. S. Finch, P. D. Blischak, B. L. Sutherland, and M. S. Barker. 2021. Patterns and processes of diploidization in land plants. Annual Review of Plant Biology in press.
Preprint: https://doi.org/10.5281/zenodo.3964504
DOI: https://doi.org/10.1146/annurev-arplant-050718-100344

Wang, B., S. Shu, Z. Li, C. Song, D. Liu, Y. Niu, J. Liu, J. Zhang, H. Liu, Z. Hu, B. Huang, X. Liu, W. Liu, L. Jiang, M. Alami, Y. Zhou, Y. Ma, X. He, Y. Yang, T. Zhang, H. Hu, M. S. Barker, S. Chen, X. Wang, and J. Nie. 2021. The Coptis chinensis genome and diversification of protoberberine-type alkaloids. Nature Communications in press.

Hao, Y., M. E. Mabry, P. Edger, M. Freeling, C. Zheng, L. Jin, R. VanBuren, M. Colle, H. An, R. S. Abrahams, X. Qi, K. Barry, C. Daum, S. Shu, J. Schmutz, D. Sankoff, M. S. Barker, E. Lyons, J. C. Pires, and G. C. Conant. 2021. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Research in press.
bioRxiv https://www.biorxiv.org/content/10.1101/2020.08.10.245258v1
DOI: https://doi.org/10.1101/gr.270033.120

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst. 2021. Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks. Molecular Ecology Resources in press.
bioRxiv preprint: https://doi.org/10.1101/2020.06.29.159673
DOI: https://doi.org/10.1111/1755-0998.13355

Qi, X., H. An, T. E. Hall, C. Di, P. D. Blischak, M. T. W. McKibben, Y. Hao, G. C. Conant, J. C. Pires, and M. S. Barker. 2021. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. New Phytologist 230: 372–386.
bioRxiv preprint: https://doi.org/10.1101/842351
DOI: https://doi.org/10.1111/nph.17194

Marx, H. E., S. A. Jorgensen, E. Wisely, Z. Li, K. M. Dlugosch, and M. S. Barker. 2021. Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest. Applications in Plant Sciences 9: e11409.
bioRxiv preprint: https://doi.org/10.1101/2020.03.31.018945
DOI: https://doi.org/10.1002/aps3.11409

2020

Román-Palacios, C., Y. F. Molina-Henao, and M. S. Barker. 2020. Polyploidy increases overall diversity despite higher turnover than diploids in the Brassicaceae. Proceedings of the Royal Society B 287: 20200962.
bioRxiv preprint: https://doi.org/10.1101/717306
DOI: https://doi.org/10.1098/rspb.2020.0962

Marx, H. E., S. Scheidt, M. S. Barker, and K. M. Dlugosch. 2020. TagSeq for gene expression in non-model plants: a pilot study at the Santa Rita Experimental Range NEON core site. Applications in Plant Sciences 8: e11398.
bioRxiv preprint: https://doi.org/10.1101/2020.04.04.025791
DOI: https://doi.org/10.1002/aps3.11398

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst. 2020. Inferring the demographic history of inbred species from genome-wide SNP frequency data. Molecular Biology and Evolution 37: 2124–2136.
bioRxiv preprint: https://doi.org/10.1101/2019.12.20.881474
DOI: https://doi.org/10.1093/molbev/msaa042

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. 2020. Sequencing and analyzing the transcriptomes of a thousand plant species across the tree of life for green plants. Annual Review of Plant Biology 71:741–765. https://www.annualreviews.org/doi/full/10.1146/annurev-arplant-042916-041040

Lv, Q., J. Qiu, J. Liu, Z. Li, W. Zhang, Q. Wang, J. Fang, J. Pan, Z. Chen, W. Cheng, M. S. Barker, X. Huang, X. Wei, and K. Cheng. 2020. The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis. The Plant Journal 103: 1910–1923.
DOI: https://doi.org/10.1111/tpj.14874

Mabry, M. E., J. M. Brose, P. D. Blischak, B. Sutherland, W. T. Dismukes, C. A. Bottoms, P. P. Edger, J. D. Washburn, H. An, J. C. Hall, M. R. McKain, I. Al-Shehbaz, M. S. Barker, M. E. Schranz, G. C. Conant, and J. C. Pires. 2020. Phylogeny and multiple independent whole-genome duplication events in the Brassicales. American Journal of Botany 107: 1148–1164.
bioRxiv preprint: https://doi.org/10.1101/789040
DOI: https://doi.org/10.1002/ajb2.1514

Li, F.-W., T. Nishiyama, M. Waller, E. Frangedakis, J. Keller, Z. Li, N. Fernandez-Pozo, M. S. Barker, T. Bennett, M. A. Blázquez, S. Cheng, A. C. Cuming, J. de Vries, S. de Vries, P.-M. Delaux, I. S. Diop, J. Harrison, D. Hauser, J. Hernández-García, A. Kirbis, J. C. Meeks, I. Monte, S. K. Mutte, A. Neubauer, D. Quandt, T. Robison, M. Shimamura, S. A. Rensing, J. C. Villarreal, D. Weijers, S. Wicke, G. K. -S. Wong, K. Sakakibara, and P. Szövényi. 2020. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nature Plants 6: 259–272.
DOI: https://doi.org/10.1038/s41477-020-0618-2

Li, Z. and M. S. Barker. 2020. Inferring putative ancient whole genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions. GigaScience 9: giaa004.
bioRxiv preprint: https://doi.org/10.1101/735076.
DOI: https://doi.org/10.1093/gigascience/giaa004

Baniaga, A. E., H. E. Marx, N. Arrigo, and M. S. Barker. 2020. Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives. Ecology Letters 23: 68–78.
bioRxiv preprint: https://doi.org/10.1101/406314.
DOI: https://doi.org/10.1111/ele.13402

2019

Carpenter, E J., N. Matasci, S. Ayyampalayam, S. Wu, J. Sun, J Y, Fabio R. J. Vieira, C. Bowler, R. G. Dorrell, M. A. Gitzendanner, Ling Li, Wensi Du, K. K. Ullrich, N. J. Wickett, T. J. Barkmann, M. S. Barker, J. H. Leebens-Mack, G. K.-S. Wong. 2019. Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). GigaScience 8: giz126 https://doi.org/10.1093/gigascience/giz126

One Thousand Plant Transcriptomes Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574: 679–685.
DOI: https://www.nature.com/articles/s41586-019-1693-2
UA News Arizona Daily Star KJZZ

Baniaga, A. E. and M. S. Barker. 2019. Nuclear genome size is positively correlated with median LTR-RT insertion time in fern and lycophyte genomes. American Fern Journal 109: 248–266.
bioRxiv preprint https://doi.org/10.1101/571570
DOI: https://doi.org/10.1640/0002-8444-109.3.248

Wolf, P. G. and M. S. Barker. 2019. Current status and future prospects for fern and lycophyte genomics: introduction to an American Fern Journal special issue. American Fern Journal 109: 177–182.
DOI: https://doi.org/10.1640/0002-8444-109.3.177

An, H., X. Qi, M. Gaynor, Y. Hao, S. Gebken, M. Mabry, A. McAlvay, G. Teakle, G. C. Conant, M. S. Barker, T. Fu, B. Yi, and J. C. Pires. 2019. Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. Nature Communications 10: 2878.
DOI: https://doi.org/10.1038/s41467-019-10757-1

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.
DOI: https://doi.org/10.1073/pnas.1819227116

2018

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.
DOI: https://doi.org/10.1093/gbe/evy200

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.
DOI: https://doi.org/10.1038/s41477-018-0188-8

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.
DOI: https://doi.org/10.1002/ajb2.1060

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. 
PNAS doi: 10.1073/pnas.1710791115 
bioRxiv doi: 10.1101/253609
UA News SUNY ESF News

Barker, M. S. 2018. A Gneato nuclear genome. Nature Plants doi:10.1038/s41477–018–0102–4.
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2017

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.
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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.

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.
PDF bioRxiv Preprint

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 303: 727–744.
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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.
PDF bioRxiv Preprint

2016

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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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. 
DOI: https://doi.org/10.3732/ajb.1600272

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.
DOI: https://doi.org/10.3732/ajb.1600113

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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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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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.
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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

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. 
PDF Science Genome Web UA News KJZZ Radio

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. 
PDF UM News NPR Washington Post PBS

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

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. 
PDF UA News Science Daily

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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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

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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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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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. 
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2012

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. 
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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. 
PDF R2G2 Tutorial

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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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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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

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

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. 
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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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Der, J. P., M. S. Barker, N. J. Wickett, C. W. DePamphilis, and P. G. Wolf. 2011. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 12: 99. 
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2010

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. 
PDF EvoPipes Repository

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. 
PDF Supplemental Data SCBG Press Release

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

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. 
PDF Supplemental Data

Barker, M. S. and P. G. Wolf. 2010. Unfurling fern biology in the genomics age. BioScience 60(3): 177–185. 
PDF Utah State Press Release

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

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. 
PDF Supplemental Data

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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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. 
PDF IU Press Release Nature Highlight Faculty of 1000

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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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.
^Co-first authors 
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2008

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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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.

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

Brandvain, Y.^, M. S. Barker^, and M. J. Wade. 2007. Gene co-inheritance and gene transfer. Science 315: 1685. 
^Co-first authors
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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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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.

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. 
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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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Barker, M. S. 2005. A Natural History of Ferns by Robbin C. Moran. American Fern Journal 95(3): 128–129. 
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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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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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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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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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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.

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.