News

New people, pictures, publications, and other activity. Move your cursor over each image for information and links.

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Congratulations, Matt Parks! Matt recently accepted a position as an Assistant Professor in the Department of Biology at Central Oklahoma University

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Click here to check out our preprint describing a kit to enrich 353 nuclear genes from any angiosperm. The kit is available for a reduced cost at Arbor Biosciences.

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Wishing Tania the best in her new position as a Data Scientist for the City of San Francisco - Congratulations, Tania!!

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Congratulations to Matt Johnson, who will be taking his waffle talents to Texas Tech as an Assistant Professor starting in Fall, 2017!

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Norm and the Matts enjoying the 115 degree heat index in Shenzhen for the International Botanical Congress, 2017

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Engaging the public with a moss table at the celebration of World Environment Day at the Chicago Botanic Garden

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Matt Johnson, Elliot Gardner, and Norm recently led a HybSeq workshop at Kew. Thank you to Lisa Pokorny for being such
a great host!

Click here to view some of the workshop materials.

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No big deal. Just an Adiantum collected by Darwin (Kew herbarium).

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Elliot enjoying the company
of cacti at Kew.
That's Elliot way over on the right.

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Bioinformatics and bocce:
A natural combination.

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HybPiper, a modular pipeline for processing target enrichment data is now available!

Click here for the pipeline and here for the paper in APPS.

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Bryologists doing what bryologists do. The Nitztal, Germany.

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The lab taking a mid-day break to see the noon showing of
Rogue One

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Titan arum twins at the Chicago Botanic Garden!

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Donut Day! For our holiday lab excursion, we did a donut tour of downtown Chicago. The post-tour analysis showed that the Donut Vault has the best donuts in town.

Collection site in the Scottish highlands of the underground liverwort Aneura mirabilis, the only non-photosynthetic bryophyte.

People

Interested in joining us? Send Norm an email to find out about opportunities in the lab: nwickett@chicagobotanic.org.

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Norm Wickett

PhD (2007) University of Connecticut
I'm interested in understanding life history evolution in bryophytes, and the application of phylogenomics and comparative genomics to the study of plant diversification. I use gene trees, transcriptomics, and draft genome sequencing to understand how processes such as gene-family diversification (possibly through whole-genome duplication), shifts in selection, and horizontal gene transfer have influenced the evolution of land plants.

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Colby Witherup

MS (2013) Northwestern University
I'm interested in the possibility of selection on meiosis and related genes in pre- and post-polyploid plant populations. I am currently examining the evolutionary history of meiosis-related genes in sequenced plant genomes to identify patterns of conservation and change across the plant phylogeny.

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Christina Shehata

BA (2019) Northwestern University
Christina is working closely with Colby to adapt genomic selection scans for use with discrete gene data. She is currently applying this in a conservation context for Brighamia, an endangered Hawaiian Islands Lobelioid.

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You?

Positions Available
Please contact Norm if you are interested in postdoc, graduate, or undergraduate opportunities in the lab!

Lab Alumni

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Matt Parks

PhD (2011) Oregon State
Comparative genomics and transcriptomics of diatoms

Currently: Assistant Professor in the Department of Biology at Central Oklahoma University

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Tania Jogesh

PhD (2014) University of Illinois
Chemical Ecology and Evolution of Onagraceae

Currently: Data Scientist for the City of San Francisco

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Matt Johnson

PhD (2013) Duke University
Former postdoc on the Moss Tree of Life project

Currently: Assistant Professor in the Department of Biological Sciences at Texas Tech University

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Rick Overson

PhD (2011) Arizona State
Former postdoc on the Landscapes of Linalool (Dimensions) project

Currently: Researcher in the Cease Lab at Arizona State University

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Claire Malley

MA (2016) Northwestern University
Methods in Orthology Detection and Application to the Moss Phylogeny

Currently: Bioinformatician at Johns Hopkins University

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Kristen Laricchia

MA (2014) Northwestern University
Transcriptome Analysis of Domesticated Breadfruit and its Wild Relatives

Currently: Associate Computational Biologist at the Broad Institute

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Laura Briscoe

MA (2012) Northwestern University
Using Molecules and Morphology to Better Understand the Liverwort Family Acrobolbaceae

Currently: Collections Manager, Steere Herbarium, New York Botanical Garden

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Lindsey Bechen

BA (2016) Amherst College
Floral morphology and patterns of gene expression associated with floral fragrance variation

Currently: Research Assistant at the Chicago Botanic Garden

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Amanda Patsis

BA (2017) Amherst College
A phylogenomic approach to inferring relationships in Oenothera sect. Pachylophus

Currently: Project Manager at Epic

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Anni Wang

BA (2018) Florida State
Comparative analysis of rates of protein conservation and divergence in diatom genomes

Currently: Fourth year student at Florida State University

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Marissa Ashner

Illinois Institute of Technology
Positional conservation of introns throughout diatom evolution

Currently: Fourth year student at Illinois Institute of Technology

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Nina Denne

Illinois Math & Science Academy
Characterization of transposable elements in diatom genomes

Currently: First year student at Carleton College


Buxbaumia aphylla, a moss with a massive sporophyte and highly reduced gametophyte.

Projects

We work with a diversity of organisms in the Wickett Lab including (but not limited to) bryophytes, diatoms, and angiosperms. We also use a diversity of methods, but all of our projects include a high-throughput sequencing component, phylogenetic methods (gene trees and species trees) and a significant amount of bioinformatics. All of our projects share a common thread - understanding the molecular processes that coincide with the origin of fundamental life history traits and the relationship between these processes/traits and diversification. The primary, NSF-funded projects of the lab are described here.

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Schiedea

Unlocking the evolutionary history of Schiedea (Caryophyllaceae): rapid radiation of an endemic plant genus in the Hawaiian Islands

The primary aim of this project is to reconstruct the pattern of breeding system evolution in Schiedea through an integrated program of field, laboratory, and genomic studies. Nuclear genome sequencing, targeted sequence capture, GBS will be used to reconstruct a highly resolved phylogenetic tree of Schiedea, identify sources of phylogenetic conflict, and investigate patterns of historical introgression. The phylogenetic hypotheses developed will be used to interpret the evolution of breeding systems including transitions from hermaphroditism to dioecy, shifts from biotic to abiotic pollination, and traits associated with pollination biology (including scent and nectar production).
(Photo: Norm Wickett)


Collaborators: Ann Sakai & Steve Weller (UC Irvine), Mike Moore (Oberlin), Warren Wagner (NTBG, Smithsonian), Krissa Skogen (CBG), Lauren Weisenberger (USFWS)

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Onagraceae

Dimensions: Landscapes of Linalool – Scent mediated diversification of flowers and moths across Western North America

Plant scents are important drivers of the relationships between angiosperms and insects (herbivory, plant defense, pollination), but remain poorly integrated into our understanding of floral evolution and pollination ecology. This study examines the role of floral scent in the diversification of the western North American evening primroses (Onagraceae) and their pollinators (hawkmoths, bees) and floral and seed predators (Mompha moths). The research examines functional trait variation and selective forces in the field and experimental arrays, the genetic basis of the variation from the population to phylogenetic level using comparative genomics, and patterns of phylogenetic diversity in Onagraceae and Mompha.
(Photo: Krissa Skogen)


Collaborators: Krissa Skogen (Lead PI) & Jeremie Fant (CBG), Rachel Levin (Amherst), Rob Raguso (Cornell), Mike Moore (Oberlin), Warren Wagner (Smithsonian)

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Diatoms

Evaluating the contributions of horizontally transferred bacterial genes and endogenous duplication events to the diversification of diatoms

The goal of this project is to identify the sources of novel diatom traits, which have contributed to their extraordinary metabolic and species-level diversity. Some traits are encoded by genes acquired from distantly related bacteria, an entirely different kingdom in the tree of life. Other genes appear to have been generated by processes acting within diatom genomes. This project will generate genome-scale data for 250 phylogenetically disparate diatom species. These data will be used to: (1) infer evolutionary relationships, (2) identify the sources - whether intrinsic or extrinsic - of new genes, and (3) correlate the pattern and timing of gene acquisitions with the origins of novel traits.
(Photo: Andy Alverson)


Collaborators: Andy Alverson (University of Arkansas), Matt Parks (Central Oklahoma University)

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Mosses

Assembling the Pleurocarpous Moss Tree of Life – Resolving the rapid radiation using genomics and transcriptomics


The moss lineage Hypnanae underwent an explosive radiation following its origin 165 mya. Today, it comprises about 5,000 species, but their grouping into evolutionary units is obscure. Inferences from extensive sets of genes sampled using target enrichment and transcriptomes will provide a robust framework to further our understanding of this diverse, and ecologically important lineage. This study focuses on untangling the relationships among species, on identifying the geologic or climatic shifts that triggered these events, and on understanding the significance of morphological innovations allowing adaptations to diverse habitats.

(Photo: Blanka Shaw)


Collaborators: Bernard Goffinet (UConn), Jon Shaw (Duke), Matt Johnson (Texas Tech), Rafa Medina (Augustana, Illinois), Yang Liu (Fairy Lake Botanical Garden, Shenzhen)

The Beagle Channel. Photo taken from the Chilean island of Navarino, home of the Omora Ethnobotanical Park.

Publications

All publications listed below are linked to journal sources. Please email Norm (nwickett@chicagobotanic.org) if you are unable to access any of the linked papers.

2018

Villaverde, T, L Pokorny, S Olsson, M Rincón, MG Johnson, EM Gardner, NJ Wickett, J Molero, R Riina, I Sanmartín. 2018. Bridging the micro and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. New Phytologist 220: 636-650. OPEN ACCESS

Guillory, WX, A Onyshchenko, EC Ruck, MB Parks, T Nakov, NJ Wickett, AJ Alverson. 2018. Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta). Genome Biology and Evolution 6: 1504-1515. OPEN ACCESS

Laricchia, KM, MG Johnson, D Ragone, EW Williams, NJC Zerega, NJ Wickett. 2018. A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.). American Journal of Botany 105(5): 915-926. OPEN ACCESS

Parks, MB, T Nakov, EC Ruck, NJ Wickett, AJ Alverson. 2018. Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). American Journal of Botany 105(3): 330-347. OPEN ACCESS

Kates, HR, MG Johnson, EM Gardner†, NJC Zerega, NJ Wickett. 2018. Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus. Americal Journal of Botany 105(3): 404-416. OPEN ACCESS

Parks, MB, NJ Wickett, AJ Alverson. 2018. Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (diatoms, Bacillariophyta). Molecular Biology and Evolution 35(1): 80-93. OPEN ACCESS

Medina, R, JG Johnson, Y Liu, N Wilding, TA Hedderson, NJ Wickett, B Goffinet. 2018. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm a rapid radiation in the moss family Funariaceae. Molecular Phylogenetics and Evolution 120: 240-247.


2016-2017

Briscoe, LRE, NJC Zerega, HT Lumbsch, M Stech, E Kraichak, MJ Von Konrat, JJ Engel, NJ Wickett. 2017. Molecular, morphological, and biogeographic perspectives on the classification of Acrobolboideae (Acrobolbaceae, Marchantiophyta). Phytotaxa 319(1): 056-070.

Carvalho-Silva, M, M Stech, LH Soares-Silva, WR Buck, NJ Wickett, Y Liu, PEAS Camara. 2017. A molecular phylogeny of the Sematophyllaceae s.l. (Hypnales) based on plastid, mitochondrial, and nuclear markers, and its taxonomic implications. Taxon 66(4): 811-831.

Johnson, MG, EM Gardner, Y Liu, R Medina, B Goffinet, AJ Shaw, NJC Zerega, NJ Wickett. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7): 1600016. OPEN ACCESS

Gardner, EM, MG Johnson, D Ragone, NJ Wickett, NJC Zerega. 2016. Low-coverage, whole- genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery. Applications in Plant Sciences 4(7): 1600017. OPEN ACCESS

Johnson, MG, C Malley, B Goffinet, AJ Shaw, NJ Wickett. 2016. A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). Molecular Phylogenetics and Evolution Molecular Phylogenetics and Evolution 98: 29-40.

Honaas, LA, EK Wafula, NJ Wickett, JP Der, Y Zhang, PP Edger, NS Altman, JC Pires, JH Leebens-Mack, CW dePamphilis. 2016. Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome. PLoS ONE 11(1): e0146062. OPEN ACCESS


2014-2015

Das, M, M Fernández-Aparicio, Z Yang, K Huang, NJ Wickett, S Alford, EK Wafula, CW dePamphilis, H Bouwmeester, MP Timko, JI Yoder, JH Westwood. 2015. Parasitic plants Striga and Phelipanche dependent upon exogenous strigolactones for germination have retained genes for strigolactone biosynthesis. American Journal of Plant Sciences 6(8): 1151-1166. OPEN ACCESS

Wilson, A, NJ Wickett, P Grabowski, J Fant, J Borevitz, G Mueller. 2015. Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor with either a reference genome or simple denovo analysis. Mycologia 107(1): 217-226.

Wickett, NJ, S Mirarab, N Nguyen, T Warnow, E Carpenter, N Matasci, S Ayyampalayam, M Barker, JG Burleigh, MA Gitzendanner, BR Ruhfel, E Wafula, JP Der, SW Graham, S Mathews, M Melkonian, DE Soltis, PS Soltis, NW Miles, CJ Rothfels, L Pokorny, AJ Shaw, L DeGironimo, DW Stevenson, B Surek, JC Villarreal, B Roure, H Philippe, CW dePamphilis, T Chen, MK Deyholos, RS Baucom, TM Kutchan, MM Augustin, J Wang, Y Zhang, Z Tian, Z Yan, X Wu, X Sun, G Ka-Shu Wong, J Leebens-Mack. 2014. A phylotranscriptomics analysis of the origin and diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America 111(14): E4859-E4868. OPEN ACCESS

Matasci, N, LH Hung, Z Yan, EJ Carpenter, NJ Wickett, S Mirarab, N Nguyen, T Warnow, S Ayyampalayam, M Barker, JG Burleigh, MA Gitzendanner, E Wafula, JP Der, CW dePamphilis, B Roure, H Philippe, BR Ruhfel, NW Miles, SW Graham, S Mathews, B Surek, M Melkonian, DE Soltis, PS Soltis, C Rothfels, L Pokorny, AJ Shaw, L DeGironimo, DW Stevenson, JC Villarreal, T Chen, TM Kutchan, M Rolf, RS Baucom, MK Deyholos, R Samudrala, Z Tian, X Wu, X Sun, Y Zhang, J Wang, J Leebens-Mack, G Ka-Shu Wong. 2014. Data access for the 1000 Plants (1KP) pilot. Gigascience 3:17. OPEN ACCESS

Kessenich, CR, EC Ruck, AM Schurko, NJ Wickett, AJ Alverson. 2014. Transcriptomic insights into the life history of bolidophytes, the sister lineage to diatoms. Journal of Phycology 50(6): 977-983.


2012-2013

Wicke, S, KF Müller, CW dePamphilis, D Quandt, NJ Wickett, Y Zhang, SS Renner, GM Schneeweiss. 2013. Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family. The Plant Cell 25(10): 3711-3725. OPEN ACCESS

Villarreal, JC, LL Forrest, NJ Wickett, B Goffinet. 2013. The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): Phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain. American Journal of Botany 100(3): 467-477.

Zhang, Y, M Fernandez-Aparicio, EK Wafula, M Das, Y Jiao, NJ Wickett, LA Honaas, PE Ralph, MF Wojciechowski, MP Timko, JI Yoder, JH Westwood, CW dePamphilis. 2013. Evolution of a horizontally acquired legume gene, albumin 1, I the parasitic plant Phelipanche aegyptiaca and related species. BMC Evolutionary Biology 13:48. OPEN ACCESS

Bliss, BJ, S Wanke, A Barakat, S Ayyampalayam, NJ Wickett, PK Wall, Y Jiao, L Landherr, PE Ralph, Y Hu, C Heinhuis, J Leebens-Mack, K Arumuganathan, SW Clifton, SN Maximova, H Ma, CW dePamphilis. 2013. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. BMC Plant Biology 13:13. OPEN ACCESS

Honaas, LA, EK Wafula, Z Yang, JP Der, NJ Wickett, NS Altman, CG Taylor, JI Yoder, MP Timko, JH Westwood, CW dePamphilis. 2013. Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biology 13:9. OPEN ACCESS

Merckx, VSFT, JV Freudenstein, J Kissling, MJM Christenhusz, RE Stotler, B Crandall-Stotler, NJ Wickett, PJ Rudall, HM de Kamer, PJM Maas. 2013. Taxonomy and Classification In Merckx, V (Ed.) Mycoheterotrophy: The Biology of Plants Living on Fungi. Springer, 356pp.

Fernández-Aparicio, M, K Huang, EK Wafula, LA Honaas, NJ Wickett, MP Timko, CW dePamphilis, JI Yoder, JH Westwood. 2013. Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful fo normalization of gene expression values during Striga hermonthica development. Molecular Biology Reports 40(4): 3395-3407.

Jiao, Y, J Leebens-Mack, S Ayyampalayam, JE Bowers, MR McKain, J McNeal, M Rolf, DR Ruzicka, E Wafula, NJ Wickett, X Wu, Y Zhang, J Wang, Y Zhang, EJ Carpenter, MK Deyholos, TM Kutchan, AS Chanderbali, PS Soltis, DW Stevenson, R McCombie, JC Pires, G Wong, DE Soltis, CW dePamphilis. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13: R3. OPEN ACCESS

McKain, MR, NJ Wickett, Y Zhang, S Ayyampalayam, WR McCombie, MW Chase, JC Pires, CW dePamphilis, J Leebens-Mack. 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany 99(2): 397-406.

Bandaranayake, PCG, A Tomilov, NB Tomilova, QA Ngo, NJ Wickett, CW dePamphilis, JI Yoder. 2012. The TvPirin gene is necessary for haustorium development in the parasitic plant Triphysaria versicolor. Plant Physiology 158(2): 1046-1053. OPEN ACCESS

Westwood, JW, CW dePamphilis, M Das, M Fernandez-Aparicio, LA Honaas, MP Timko, NJ Wickett, JI Yoder. 2012. The Parasitic Plant Genome Project: New tools for understanding the biology of Orobanche and Striga. Weed Science 60(2): 295-306.


2010-2011

Wickett, NJ, LA Honaas, EK Wafula, M Das, K Huang, B Wu, L Landherr, MP Timko, J Yoder, JH Westwood, CW dePamphilis. 2011. Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis. Current Biology 21(24): 2098-2104. OPEN ARCHIVE

Wickett, NJ, LL Forrest, JM Budke, B Shaw & B Goffinet. 2011. Frequent pseudogenization and loss of the plastid-encoded, sulfate transport gene cysA throughout the evolution of liverworts. American Journal of Botany 98(8): 1263-1275.

Hsu CY, JP Adams, H Kim, K No, C Ma, SH Strauss, J Drnevich, L Vandervelde, JD Ellis, BM Rice, NJ Wickett, LE Gunter, GA Tuskan, AM Brunner, GP Page, A Barakat, JE Carlson, CW dePamphilis, DS Luthe & C Yuceer. 2011. FLOWERING LOCUS T Duplication Coordinates Reproductive and Vegetative Growth in Perennial Poplar. Proceedings of the National Academy of Sciences of the United States of America 108(26): 10756-10761.OPEN ACCESS

Jiao Y, NJ Wickett, S Ayyampalayam, A Chanderbali, L Landherr, PE Ralph, LP Tomsho, Y Hu, H Liang, PS Soltis, DE Soltis, SW Clifton, SE Schlarbaum, SC Schuster, H Ma, J Leebens-Mack & CW dePamphilis. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.

Der JP, MS Barker, NJ Wickett, CW dePamphilis & PG Wolf. 2011. De novo Characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 99:12. OPEN ACCESS

Forrest LL, NJ Wickett, CJ Cox & B Goffinet. 2011. Deep sequencing of Ptilidium pulcherrimum suggests evolutionary stasis in liverwort chloroplast structure. Plant Ecology and Evolution 144(1): 29-43.

Liang H, S Ayyampalayam, NJ Wickett, A Barakat, Y Xu, L Landherr, P Ralph, T Xu, SE Schlarbaum, H Ma, JH Leebens-Mack & CW dePamphilis. 2011. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. Tree Genetics and Genomes 7(5): 941-954.

Preußing M, S Olsson, A Schäfer-Verwimp, NJ Wickett, S Wicke, D Quandt & M Nebel. 2010. New insights in the evolution of the liverwort family Aneuraceae (Metzgeriales, Marchantiophyta) with an emphasis on the genus Lobatiriccardia. Taxon 59(5): 1424-1440.

Cox CJ, B Goffinet, NJ Wickett, SB Boles & AJ Shaw. 2010. Moss diversity: a molecular phylogenetic analysis of genera. Phytotaxa 9:175-195.


2004-2009

Wickett NJ, Y Fan, PO Lewis & B Goffinet. 2008. Distribution and evolution of pseudogenes, gene losses and a gene rearrangement in the plastid genome of the non- photosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida). Journal of Molecular Evolution 67: 111-122.

Wickett NJ, Y Zhang, SK Hansen, JM Roper, JV Kuehl, SA Plock, PG Wolf, CW dePamphilis, JL Boore & B Goffinet. 2008. Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Molecular Biology and Evolution 25(2): 393-401. FREE ACCESS

Wickett, NJ, & B Goffinet. 2008. Origin and relationships of the myco-heterotrophic liverwort Cryptothallus mirabilis Malmb. (Metzgeriales, Marchantiophyta). Botanical Journal of the Linnean Society 156: 1-12.

Goffinet B, NJ Wickett, O Werner, RM Ros, AJ Shaw & CJ Cox. 2007. Distribution and phylogenetic significance of the 71 kb inversion in the chloroplast genome in the Funariidae (Bryophyta). Annals of Botany 99: 747-753. FREE ACCESS

Goffinet, B, NJ Wickett, AJ Shaw, & CJ Cox. 2005. Phylogenetic significance of the RpoA loss in the chloroplast genome of mosses. Taxon 54 (2): 353-360.

Goffinet B, AJ Shaw, CJ Cox, NJ Wickett & S Boles. 2004. Phylogenetic inferences in the Orthotrichoideae (Orthotrichaceae: Bryophyta) based on variation in four loci from all genomes. Monographs in Systematic Botany from the Missouri Botanical Garden 98:270-289.