x Updated on 07/19/2016

Robert K. Jansen, Sidney F. and Doris Blake Centennial Professor in Systematic Botany, Department of Integrative Biology, University of Texas at Austin

Birthdate: 4/23/1954 Birthplace: Green Bay, Wisconsin

Work Address: Department of Integrative Biology University of Texas at Austin Biological Laboratories 212 Austin TX 78712 Phone: 512-471-8827 (office), 512-471-8854 (lab) Fax: 512-232-9529 Email: [email protected]

Date of Appointment: 1991

Education: B.S. 1976 Univ. of Wisconsin-Oshkosh - Biology Ph.D. 1982 Ohio State University - Botany

Experience: 1976-1982 Research/Teaching Assistant, Ohio State University 1982-1983 Assistant Professor, Columbus College of Art and Design 1982-1983 Research Associate, Botany Department, Ohio State Univ. 1983-1984 Visiting Assistant Professor and Acting Curator of Beal- Darlington Herbarium, Michigan State University 1984-1987 Postdoctoral Research Fellow, Univ. of Michigan 1987-1991 Assistant Professor, Department of Ecology and Evolutionary Biology, The University of Connecticut 1991-1998 Associate Professor, Department of Botany, The University of Texas at Austin 1998-1999 Professor, Department of Botany, The University of Texas at Austin 1999- 2015 Chair, Department of Integrative Biology, The University of Texas at Austin 1999 - Professor, Department of Integrative Biology, The University of Texas at Austin 2000- Sidney F. and Doris Blake Centennial Professor in Systematic Botany 2011- Distinguished Adjunct Professor, King Abdulaziz University, Faculty of Science, Biotechnology Section, Department of Biological Sciences 2016- Director, TEX-LL Herbarium

Honors or Distinctions: B.S. Biology (cum laude) 1976, Sigma Xi member, 1977- present; ISI Highly cited.

1 Fields of Specialization: Research in my lab is concentrated in four areas: (1) organization and evolution of plastid genomes; (2) computational methods for comparative genomics, (3) coordinated evolution between mitochondrial. nuclear and plastid genomes, and (4) systematics and the evolution of the Geraniaceae and Fabaceae.

Professional Societies: American Society of Plant Taxonomists, Botanical Society of America, International Association of Plant Taxonomists, Society for the Study of Evolution, Society of Systematic Biology

National and International Offices:

1983-1984 ASPT Committee for Floristics of Temperate North America, Acting Chairman 1988-1989 ASPT Nominations Committee member 2001- Editorial Committee, Systematic Botany 1996-1999 Council Member, ASPT 1996-1999 ASPT Awards Committee 1990- Advisory Board, Plant Systematics and Evolution 1990- Editorial Board, Biochemical Systematics and Ecology 1998-2001 Member, Committee of Visitors, Arnold Arboretum, Harvard Univ. 1998-2001 Editorial Board, Journal of Plant Biology 2001- Scientific Advisory Board, Seacology 2005 ASPT Local host of Annual Meetings 2005- BMC Evolutionary Biology, Editorial Board 2007- Editorial Board, Journal of Plant Biology 2010 - Advisory Committee of Biodiversity Research Center, Academia Sinica, Member

Manuscript Reviews:

American Journal of Botany Annals of Botany Annals of the Entomological Society of America Annals of the Missouri Botanical Garden Biochemical Systematics and Ecology Biological Journal of the Linnaean Society BMC Evolutionary Biology BMC Genomics BMC Plant Biology Brittonia Canadian Journal of Botany C R Biologies Current Plant Biology DNA Research Evolution Frontiers in Ecology and Evolution Frontiers in Plant Science

2 Genetics Genome Biology and Evolution Genome Research Journal of Molecular Evolution Lundellia Molecular Biology and Evolution Molecular Ecology Molecular Phylogenetics and Evolution National Geographic Society Nature New Phytologist New Zealand Journal of Botany Photosynthesis Research Plant Biotechnology Journal Plant Cell Plant Cell Reports Plant Molecular Biology Plant Systematics and Evolution Planta PloS One Proceedings of the National Academy of Science Science Systematic Biology Systematic Botany Systematic Botany Monographs Taxon Trends in Genetics Nucleic Acids Research

Grant Reviews

National Science Foundation: Systematic Biology Population Biology New Young Investigators - panel member (1993) Committee of Visitors - Systematics and Population Biology Cluster - member (1993) NSF/DOE/USDA Collaborative Research in Plant Biology Panel (1994) Systematic Biology Panel Member (1997,1998, 2000) National Geographic Society

Past Graduate Students:

Linda Raubeson, Ph.D. 1992 Yale - currently an Associate Professor at Central Washington University Roberta Mason-Gamer, Ph.D. 1993 University of Connecticut - currently an Associate Professor at University of Illinois at Chicago Mary Beth Cosner, Ph.D. 1993 Ohio State University - deceased Jeannette Whitton, Ph.D. 1994 University of Connecticut - currently an Associate

3 Professor at the University of British Columbia Youngdong Kim, Ph.D. 1994 Univeristy of Texas - currently an Associate Professor at Han Lim University, Korea Alice Hempel, Ph.D. 1995 Univ. of Texas - Associate Professor at Texas A&M Kingsville Dennis Loockerman, Ph.D. 1996 Univeristy of Texas - currently employed in the DNA fingerprinting lab in the Texas Department of Public Safety Kathy Gould Mathews, Ph.D. 1997 University of Texas - currently an Assistant Professor at Western Carolina University Hyi-Gyung Kim, Ph.D. 1997 University of Texas - currently a Research Associate at the University of Texas Carolyn Ferguson, Ph.D. 1998 University of Texas, currently an Associate Professor at Kansas State University Zaiming Zhao, Ph.D. 1999 University of Texas, currently a Lecturer in the School of Biological Sciences at University of Texas Doug Goldman, Ph.D. 2000 University of Texas, currently a Research Assistant at Harvard University Jan Barber, Ph.D. 2000 University of Texas, currently an Associate Professor at Saint Louis University Les Goertzen, Ph.D. 2001 University of Texas, currently an Associate Professor at Auburn University. Sarah Simmons, Ph.D. (co-advisor with Beryl Simpson) 2002 University of Texas, currently the Program Coordinator of Undergraduate Research, College of Natural Sciences, University of Texas. Katie Hansen, Ph.D. 2004 University of Texas, currently a Lecturer and Research Fellow at University of Texas. Stacia Wyman, Ph.D. (co-advisor with Ben Kuipers, computer science) 2004 University of Texas, currently a postdoctoral fellow at Fred Hutchinson Cancer Institute, Seattle, Washington. Bonnie Crozier, Ph.D. (co-advisor with Jose Panero) 2005 University of Texas, currently a research fellow at University of Texas. Mike Moore, Ph.D. 2005 University of Texas, currently an Assistant Professor at Oberlin College. Romey Haberle, Ph.D. 2006 University of Texas, currently an Assistant Professor at Pacific Luthern University. Barbara Goodson, Ph.D. 2007. University of Texas, currently a Research Fellow at Tennessee Tech University. Timothy Chumley, Ph.D. 2007. University of Texas, currently an environmental consultant in San Diego CA. Mary Guisinger, Ph.D. 2009. University of Texas, Microsoft. Pamela Steele, Ph.D. 2009. University of Texas, currently an Assistant Professor at University of Nebraska at Omaha. Zhengqiu Cai, Plant Biology, Ph.D. 2010. University of Texas, currently a bioinformatician at Harvard Medical School Debra Hansen (co-advised with Beryl Simpson), Plant Biology, Ph.D. 2012, currently a lecturer in the School of Biological Sciences, UT-Austin. Taylor Sultan Quedensley, Plant Biology, Ph.D. 2012, currently an Assistant Professor at Missouri Western University. Michael Gruenstaeudl, Plant Biology Ph.D., 2013, currently a postdoctoral fellow

4 at Free University of Berlin. John C, Blazier, Plant Biology PhD., 2013, currently a postdoctoral fellow at Texas A & M University Maolun Weng, Plant Biology PhD., 2015, currently a postdoctoral fellow at the University of Maryland. Jin Zhang, Plant Biology PhD., 2015, currently a software engineer at Pinterest, San Francisco CA Erika Schwarz, Plant Biology, PhD., 2016, currently Assistant Professor at Austin Community College

Current Graduate Students:

Anna Yu, Ph.D. candidate, Plant Biology, co-advisor with Ed Theriot Chaehee Lee, Ph.D., Plant Biology Bikash Shrestha, Ph.D., Plant Biology Deise Josely Pereira Gonçalves, Ph.D. candidate, Plant Biology Aldanah Alqahtani, MS., Plant Biology

Postdoctoral Fellows:

Dr. Robert S. Wallace - Rutgers University - Oct 1987- Aug 1990 Dr. Jan Johannson - University of Lund - Sep 1989 - Jun 1990 Dr. Ki-Joong Kim - University of Texas - Dec 1989 - Aug 1994 Dr. Linda Raubeson - Yale University - May 1991 - Dec 1991 Dr. Jose Panero - University of Tennessee - Jun 1991- Dec 1993 Dr. Jun Wen - Ohio State University - Mar 1991 - Dec 1991 Dr. Javier Fuertes - Univ. of Salemanca, Spain - Oct 1994 - Jun 1996 Dr. Javier Francisco-Ortega - Univ. of Birmingham, Great Britain - Jan 1994 - Dec 1996 Dr. Juli Caujape-Castells - University of Barcelona, Spain - Jan 1997 - Sep 1998 Dr. Seonjoo Park - Korea University, Korea - Sep 1998 - May 2000. Dr. William Eddie - University of Edinburgh - Apr 2000 - Sep 2003 Dr. Tracey Ruhlman – University of Central Florida – July 2009 – May 31, 2011 Dr. Seongjun Park – Yeungnam University, Korea – November 5, 2012 – November 30, 2014. Dr. Matt Ashworth – University of Texas at Austin – Feb 2015 – present.

Research Associates:

Dr. Tracey Ruhlman – June 1, 2011 – present

Visiting Scientists:

Dr. Birgitta Bremer - University of Stockholm - Fall 1987 Dr. Edward Schilling - University of Tennessee - Spring 1988 Ms. Linda Watson - University of Oklahoma - Spring 1988 Mr. Ki-Joong Kim - University of Texas - Summer 1988 Dr. Sterling Keeley - Whittier College - Aug 1988 - Aug 1990 Ms. Linda Raubeson - Yale University - Aug 1988 - Apr 1991

5 Dr. Meredith Lane - Univ. of Kansas - Aug 1989 - Dec 1989 Dr. Lowell Urbatsch - Louisiana State University - 1991 Dr. Mari Kallerjso - Smithsonian Institution - Nov 1991 Dr. Mark Bierner - Southwest Texas State University - Jun 1992 - Jun 1993 Dr. John Averett - National Wildflower Research Center - Aug 1992 - Aug 1994 Dr. Luc Brouillet - University of Montreal - Jan 1993 - Apr 1993 Dr. Frank Hellwig - University of Gottingen - Jul 1993 - Dec 1993 Mr. Liu Jianguo - Xinjiang Agricultural College - Aug 1994 - Aug 1995 Dr. Uta-Regina Boehle - Freie Universitat Berlin - Dec 1996 - Jan 1997 Dr. John Bain - University of Lethbridge - Jan 1993 - Jul 1993, Jan 1997 - Jun 1997 Ruth Jaen Molina – Jardín Botánico Canario "Viera y Clavijo", Mar – Dec 2001 Dr. Ki-Ryong Park - Kyung-Nam University, Mar 2004 - Feb 2005 Dr. Stephen Downie - University of Illinois, Jan - June 2008 Dr. Seonjoo Park - Yeungnam University, August 2010 – July 2011.

Undergraduate Research Advising:

Elisa Korompai - Summer - Fall 1993 -"Phylogenetic Relationships in the tribe Lactuceae (Asteraceae) Using ndhF Sequences" -funded by a REU supplement to NSF grant Marianela Cuadrado - Summer 1993 - "Molecular Phylogenetic Studies in Passiflora (Passifloracae)" - funded by a REU supplement to an NSF grant to Dr. Linda Escobar at the University of Puerto Rico Fernanda Zermoglio - Fall - Spring 1994 "Phylogenetic Studies of the tribe Mutisieae (Asteraceae)" Ayelet Hines - Summer - Fall 1995 - "Phylogenetic Relationships of Argyranthemum (Asteraceae)" - funded by an REU supplement to my NSF grant Susan Chen - Fall - Spring 1996 - "Origin of the Crop Plant Pepino Based on Nuclear DNA Sequences" - funded by University of Texas Undergraduate Research Funds Scott McGauley - Fall - Spring 1996 - "Morphological and Molecular Studies of Ibervillea (Cucubitaceae) in Texas" Franziska Kramer - Spring 1997 - "Molecular Systematic Studies of Phlox (Polemoniaceae)" - Franziska was an exchange student from Germany Kyla Hobbs - Spring 1997 - "A Data-base of Useful Wild Plants of Texas" Cindy Lintz - Fall 1997-Spring 1998 - "DNA Studies of Endemic Macaronesian Asteraceae" - funded by a REU supplement to my NSF grant Jeff Mower - Spring/Summer 1998 - "ndhF Sequence Variation in the Inuleae" - funded by a REU supplement to my NSF grant Josh Egly – Summer - Fall 1999 – “ETS Sequence Variation in Tolpis (Asteraceae)”- funded by a REU supplement to my NSF grant Kavita Vyas - Fall 2000 -"ITS Sequence Variation in the Campanulaceae" - funded by a REU supplement to my NSF grant Christine Green – Summer 2001 – present “Molecular Phylogeny of Echium” Michael Martinez - Summer 2002 - "Chloroplast genome sequencing of Pelargonium" Ashley Dang - Spring 2002 - Spring 2003 "matK sequences and the phylogeny of Campanulaceae Tammy Lee - Fall 2002 - Spring 2004 "rbcL sequences and the phylogeny of Campanulaceae Vanity McMurtry - Fall 2003 - Spring 2004 "chloroplast genome sequencing of Trifolium

6 (Fabaceae) Cynthia Penaflor - Summer 2004/2005 - Intern from Brigham Young University "chloroplast gene sequences and the phylogeny of Campanulaceae" Sumaiyah Krehman - Fall 2004 - Spring 2006 - Phylogenetic studies in Descurainea (Brassicaceae) Heather Bruce - Fall 2006 - Spring 2007 - Chloroplast genome evolution in Geraniaceae. Lauren Friar - Summer 2007 - Summer 2008 - Phylogeny of Psiguria (Cucurbitaceae). Valerie Mize - Fall 2007 - 2008 - Multigene phylogeny of Geraniaceae Romey Inman – Fall 2009 – Spring 2010 - Multigene phylogeny of Geraniaceae. Suwetha Amsavelu – Spring 2011 – Spring 2012 – genome evolution in Geraniaceae. Madhu Govindu – Spring 2011 – 2014 – genome evolution in Geraniaceae. Angela Chia-Chi Fu – Spring 2013 – Fall 2014– genome evolution in Geraniaceae. Bernice Nga Fong Yau – Spring 2013 – Fall 2014– genome evolution in Geraniaceae.

Graduate Student Committees:

Matt Ashworth, Ph.D. - Plant Biology Teofil Nakov, Ph.D. - Plant Biology Gary Baird, Ph.D. - Botany Hyong-Ha Kim, Ph.D. - Botany Todd Barkman, Ph.D. - Botany Jae-Hyun Kim, Ph.D. - Microbiology Phyllis Boyd, M.S. – Botany Younseok Kweon, Ph.D. - Zoology Mariska Brady, Ph.D. – Plant Biology Edgardo Ortiz, Ph.D. – Plant Biology Yu-Fen Chen, M.S. - Biology James V. Landrum, Ph.D. - Botany Karen Clary, Ph.D. - Botany Leah Larkin, M.S. - Botany John Clement, Ph.D. - Botany Yew Lee, Ph.D. - Botany Janis Clements, M.A. - Botany Mark Mayfield, Ph.D. - Botany Xiojiang Cui, Ph.D. - Botany Josh McDill, Ph.D. - Plant Biology Jennifer Fritz, Ph.D. - Botany Heungsop Shin, Ph.D. - Botany Tony Gonzalez, Ph.D. - Plant Biology Jennifer Tate, Ph.D. - Botany Yanlin Guo, Ph.D. - Botany Martin E. Timana - Botany Tracy Heath, Ph.D. - EEB Ruth Timme, Ph.D., Plant Biology Megan Helfgott, Ph.D. - Botany Shun Tong, Ph.D. - Molecular Biology Mark Holder, Ph.D. - Molecular Biology Yoriko Uozumi, Ph.D. - Biology Amalia Diaz, Ph.D. – Plant Biology Oscar Vargas, Ph.D. – Plant Biology Hsu-Liang Hsieh, Ph.D. - Biology Li-San Wang, Ph.D. - Computer Science Kyongmin Hwang, Ph.D. - Biology Zaiming Zhao, Ph.D. - Botany Sarah Jackson, Ph.D. - Plant Biology Alicia Zicker, Ph.D. - Botany Sarah Johnson, Ph.D. - Botany Derrick Zwickl, Ph.D. - EEB Vanessa Rivera, Ph.D. – Plant Biology

Courses Taught (UT only):

Native Plants (BOT 419) Plant Systematics (BOT 362/383C) Angiosperm Diversity Lab (BOT 262C/283D) Laboratory Methods in Molecular Systematics (BOT 394C) Methods in Systematics (BOT 394) Conference Course (BOT 110C) Chloroplast Genomics (BIO 384K) Recent Advances in Plant Phylogeny (BIO 384K)

7 Genetically Modified Organisms: Environmental, Ethical, and Political Issues (UGS 302)

Departmental/Section Committees:

1992-1993 Co-organized Departmental Seminars 1994 Plant Ecology Search Committee 1995 Plant Evolution Search Committee 1995-1996 Undergraduate advisor 1994 Graduate Affairs Committee, Member 1996-1999 Head, Graduate Admissions, Botany Graduate Program 1999 Conservation Biology Search Committee, Member 2002 Uteach Search Committee, Chair 2003 Molecular Evolution Search Committee, Member 1999 – 2015 Chair, Section/Department of Integrative Biology

School of Biological Sciences Committees:

1998 – 2013 Executive Council, Member 1999 – 2013 Planning Council, Member 2000 Biostatistics Search Committee, Chair 2001 – 2013 Academic Council

University Committees:

1993-1994 College of Natural Sciences, Member, Committee for Strategic Planning of Life Sciences 1994 - 1995 College of Natural Sciences, Member, Life Sciences Reorganization Committee 1995 – 1996 College of Natural Sciences, Member, Honors Committee 1995 – 1996 College of Natural Sciences, Member, ESB Renovation Committee 1997 – 1998 College of Natural Sciences, Member, Graduate Programs Task Force for Reorganization of the Life Sciences 2012 – present College of Natural Sciences, Member Plant Growth Facilities Committee 2008 – 2010 College of Natural Sciences, BFL Task Force

Invited Lectures, Workshops, and Courses (since 1993):

12 October 1993 - Biology Department, Southwest Texas State University 20 October 1993 - Biology Department, Texas A & M University 11 - 13 January 1993 - Department of Biology, University of South Florida, Plant Molecular Systematics Workshop 18 February 1993 - Department of Ecology and Evolutionary Biology, University of Connecticut 14 July 1993 - University Rotary Club, Austin, Texas 11 November 1993 - Botany Department, Ohio University August 1993 – “Phylogenetic studies of the Asteridae based on ndhF sequences,” Symposium on Alternative Genes for Plant Phylogeny. American Institute of Biological Sciences, Ames, Iowa

8 14 October 1994 - Biology Department, University of North Dakota November 19, 1994. “The use of herbarium material for DNA studies. “ Sampling the Green World Conference, Fort Worth, Texas 11 February 1994 - Conference of the Association of Texas Botanic Gardens, University of Texas. 25 May 1994 - Botany Department, Smithsonian Institution 31 May 1994 - Department of Organismic and Evolutionary Biology, Harvard University June 1994 – “Applications of chloroplast DNA restriction site studies for conservation genetics. “ American Association for the Advancement of Science, Pacific Division, San Francisco State University June 1994 - Bio 401C, 601C and Hughes Undergraduate program, University of Texas July 1994 – “Phylogenetic implications of chloroplast DNA variation at inter- and intrafamilial levels.” Compositae Conference, Kew Botanic Gardens, England July 1994 – “Phylogeny and evolution of the Lactuceae based on chloroplast DNA data.” Compositae Conference, Kew Botanic Gardens, England 3 July - 13 July 1995 - "Curso sobre sistematics molecular en plantas", two week course at the Instituto Canario de Investigaciones Agrarias, Valle Guerra, Tenerife, Canary Islands, Spain 27 June - 10 July 1996 - "Metodos en Sistematica Molecular de Plantas", two week course at the Jardin Botanico Canario "Viera Y Clavijo", Las Palmas de Gran Canaria, Gran Canaria, Canary Islands, Spain 29 September 1996 - Department of Biology, Yeungnam University, South Korea 1 October 1996 - Korean Institute of Biological Sciences, 50th Anniversary Meeting, Seoul, South Korea 4 October 1996 - Korean Society of Plant Taxonomists, Korea University, Seoul, South Korea 23 October 1996 - Department of Botany, University of Kansas 12 March 1997 - Department of Botany and Plant Sciences, University of California- Riverside 20 May 1997 - Relevance of Phylogeny to the Biological Sciences, presented to participants of the Workshop on Teaching in Biology held at the University of Texas 26 June 1997 - Hughes Undergraduate Program, University of Texas 9 September 1997 - Department of Biology, University of Missouri-St. Louis 21 April 1998 - North Austin Rotary Club, Austin, Texas 27 March 2000 – Department of Biology, Trinity University, San Antonio, TX. Two talks: “Molecular data and the phylogeny and classification of the Asteraceae" and "Origin and evolution of endemic plants from the Macaronesian archipelagos" 4 May 2000 – Department of Biology, University of New Mexico, and "Origin and evolution of endemic plants from the Macaronesian archipelagos" 21 August 2000 - Cosner, M.E, R. K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. 2000. A new fast heuristic for computing the breakpoint phylogeny and experimental analyses of real and synthetic data. 8th International Conference on Intelligent Systems for Molecular Biology, La Jolla, CA, USA 23 September 2000 - Cosner, M.E, R. K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. 2000. An empirical comparison of

9 phylogenetic methods on chloroplast gene order in Campanulaceae, DCAF meetings, Montreal, Canada 2 November 2000 – Jansen, R. K. 2000. DNA markers for assessing phylogenetic relationships among plant species. NIEH workshop on “PCR-based approaches to identify and quantitate botanicals in dietary supplements, Research Triangle Park, North Carolina 14 January 2002. Jansen, R. K,. Comparative Chloroplast Genomics: Computational Methods for Reconstructing Phylogenies Using Genomic Rearrangements. Workshop on Integration of Phlygenetics and Genomics, Plant, Animal & Microbe X Conference, San Diego, CA 13 January 2003. Jansen, R. K. Comparative Chloroplast Genomics: Integrating Computational Methods, Phylogeny, and Molecular Evolution. Workshop on Organellar Genetics, Plant, Animal & Microbe XI Conference, San Diego, CA 11-15 January 2003. Jansen, R.K. Comparative chloroplast genomics: integrating computational methods, phylogeny, and molecular evolution. Plant Animal Genomics XI, San Diego, California 3 August 2004. Jansen, Robert K., Claude de Pamphilis, Linda A. Raubeson, James Leebens-Mack, Liying Cui, Yan Zhang, Stacia Wyman, Jeffrey Boore, and Jennifer V. Kuehl. The utility of whole chloroplast genome sequencing for reconstructing deep nodes in plants with an example from basal angiosperms. Symposium on Methods and Theory of Phylogenetic Inference, Botany 2004, Snowbird, Utah 4 August 2004. Haberle, Rosemarie C., Robert K.Jansen, Jeffrey L. Boore, and Jennifer Kuehl. Comparative chloroplast genomics of Campanulaceae: a model system for understanding mechanisms of genome evolution and the utility of genomic changes for phylogeny reconstruction. Symposium on Resolving the Green Branch of Life: Current Progress and Future Challenges, Botany 2004, Snowbird, Utah 6 July 2005. Jansen, R.K. Phylogenetic and Molecular Evolutionary Studies of Angioosperms Based on Whole Chloroplast Genomes. Botany Department, University of British Columbia, Vancouver, BC, Canada. 15 August 2005. Jansen, R. K. History and current status of Comparative Chloroplast Genomics. Symposium on Comparative Chloroplast Genomics, Botany 2005, Austin, TX. 17-22 September 2006. Jansen, R.K. Comparative Chloroplast Genomics. 4 lectures presented in Summer School Course course "Genome Evolution in Eukaryotes held in Bertinoro, Italy. 9 March 2007. Jansen, R.K. Phylogenetic and Molecular Evolutionary Studies of Angiosperms Based on Chloroplast Genome Sequences, Department of Biology, University of Iowa. 9 July 2007. Jansen, R.K. Comparative Chloroplast Phylogenomics: Implications for Phylogeny and Genome Evolution in Angiosperms. Symposium on Plant Phylogenomics: Defining Synergies between Plant Systematics and Genome Biology. Botany and Plant Biology 2007 Joint Congress, Chicago, Illinois. 9 December 2007. Jansen, R. K. Comparative Plastid Genomics resolves phylogenetic relationships among major angiosperm lineages and reveals genome-scale evolutionary patterns. International Symposium on Chloroplast Genomics and Genetic Engineering, Changchun, China.

10 24 March 2008. Jansen R.K. Comparative Chloroplast Genomics Resolves Relationships among Major Lineages of Flowering Plants and Reveals Genome-scale Evolutionary Patterns. Burnet School of Biomedical Sciences, University of Central Florida, Orlando FL. 6 May 2008. Jansen R.K. Comparative Chloroplast Genomics: Implications for Phylogeny and Genome Evolution in Angiosperms. Missouri Botanical Garden, St. Louis, MO. 10 November 2008. Jansen R.K. Plastid Phylogenomics: Genome Evolution in the Fast Lane. Washington University, St. Louis, MO. 17 November 2008. Jansen R.K. Plastid Phylogenomics: Fast Genomes and Deep Nodes. Louisiana State University, Baton Rouge LA. 16 March 2009. Jansen R.K. Plastid Phylogenomics: Fast Genomes and Deep Nodes. Department of Organismal and Evolutionary Biology, Harvard University. 28 March 2009. Jansen R.K. Comparative Plastid Genomics Resolves Relationships among Major Lineages of Flowering Plants and Reveals Genome-scale Evolutionary Patterns. Genes, Genomes, and Plant Evolution Symposium, Smithsonian Institution, Washington DC. 27 October 2009. Jansen R.K. Keynote Speaker – in Organelles Symposium at the 9th International Plant Molecular Biology Congress. Title: Plastid Genome Organization & Evolution in Flowering Plants. October 25-30, St. Louis MO. 9 January 2010. Jansen R.K. Invited speaker in Organellar Genetics Symposium at Plant & Animal Genomes XVIII Conference. Title: Geraniaceae, A Natural Model System for Examining Plastid Genome Evolution. January 9-13, 2010, San Diego CA. 21 June 2010. Invited Speaker and Session Co-organizer – in Genomics and Evolution I session at 2nd International Symposium on Chloroplast Genomics and Genetic Engineering. Title: Extreme Reconfiguration of the Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage. June 20-23, 2010, Maynooth, Ireland. 16 March 2011. Invited Speaker in International Conference on Island Biodiversity 2011: Present and Emerging Knowledge on the Evolution, Diversity and Conservation of the Canary Island Flora. March 14-18, 2011, Las Palmas, Gran Canaria, Canary Islands, Spain. Title: Phylogenetic Investigations of Correlated Diversification between Plants and their Associated Arbuscular Mycorrhizal Fungi in Macaronesia 28 July 2011. Invited Speaker at the International Botanical Congress 2011. Symposium on Plant genomes: not just for models anymore. Title: Geraniaceae, a natural model system for examining plastid genome evolution. 9 January 2012. Invited Speaker at the 1st Workshop for Current Research Activities of Highly Cited Professors Collaborating with KAU in the Biotechnology Program. Title: Plastid Genome Organization and Evolution in Flowering Plants. King Abdulaziz University, Jeddah, Saudi Arabia. 4 June 2012. Department of Biology, Yeungnam University, Daegu, Korea. Title: Plastid Genome Organization and Evolution in Flowering Plants. 5 June 2012. Department of Biology, Kyungpook National University, Daegu, Korea. Title: Plastid Genome Organization and Evolution in Flowering Plants. 15 June 2012. Department of Biology, Korea University, Seoul, Korea. Title: Plastid Genome Organization and Evolution in Flowering Plants. 18 November 2012. Highly Cited Program Workshop, King Abdulaziz University,

11 Jeddah, Saudi Arabia. Title: Comparative Genomics of Date Palm and Legumes: Implications for Genome Evolution of Mitochondria and Plastids. 18 November 2012. Highly Cited Program Workshop, King Abdulaziz University, Jeddah, Saudi Arabia. Title: Coordinated Evolution Across Three Plant Genomes of Geraniaceae. 9 May 2013. 3rd International Symposium on Chloroplast Genomics and Genetic Engineering, Rutgers University, New Brunswick NJ USA. Coordinated Evolution Across Three Plant Genomes of Geraniaceae. 18 January 2015. Gordon Conference “Chloroplast Biotechnology”. "Coevolution of Plastid and Nuclear Genomes". Ventura CA. 23 July 2015. Biodiversity Research Center, Academia Sinica, Taipei, Taiwan. Title: Coevolution of plastid and nuclear genomes in Geraniaceae. 6 August 2015. Department of Biological Sciences, Kwanse Gakuin University, Sanda, Japan. Title: Plastid Genome Evolution of Diatoms. 16 November 2015. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. Title: Evolutionary and Biotechnology Implications of genome variation in Rhazya stricta and legumes.

Publications:

(1) Jansen, R. K. and B. Parfitt. 1977. Allenrolfea mexicana Lundell (Chenopodiaceae): Its conspecificity with A. occidentalis (S. Wats.) Kuntze. Rhodora 79:130-132. (2) Jansen, R. K. and T. F. Stuessy. 1980. Chromosome counts of Compositae from Latin America. Amer. J. Bot. 67: 585-594. (3) Jansen, R. K. 1981. Systematics of Spilanthes (Compositae: Heliantheae). Syst. Bot. 6: 231-257. (4) Smoot, E. L., R. K. Jansen, and T.N. Taylor. 1981. A phylogenetic analysis of land plants: A botanical commentary. Taxon 30:65-67. (5) Bolick, M. and R. K. Jansen. 1981. New combinations of Salmea DC. (Compositae: Heliantheae). Brittonia 33:186. (6) Jansen, R. K., N. A. Harriman, and L. Urbatsch. 1982. Squamopappus, gen. nov., and a redefinition of Podachaenium (Compositae: Heliantheae). Syst. Bot. 7:476-483. (7) Jansen, R. K. and T. F. Stuessy. 1983. Una variedad nueva de Heliopsis (Compositae) de Colombia. Mutisia 51:1-4. (8) Jansen, R. K., T. F. Stuessy, S. D. Piedrahita, and V. A. Funk. 1984. Recuentos cromosomicos de Compositae de Colombia. Caldasia 14:7-20. (9) Jansen, R. K. 1985. Systematics of Acmella (Asteraceae: Heliantheae). Syst. Bot. Monographs 8. 115 pp. (10) Jansen, R. K. 1985. Systematic significance of chromosome numbers in Acmella (Asteraceae: Heliantheae). Amer. J. Bot. 72: 1835-1841. (11) Jansen, R. K., E. B. Smith and D. J. Crawford. 1987. A cladistic study of North American Coreopsis (Asteraceae: Heliantheae). Plt. Syst. Evol. 57: 73-84. (12) Jansen, R. K. and J. D. Palmer. 1987. Chloroplast DNA from lettuce and Barnadesia (Asteraceae): structure, gene localization, and characterization of a large inversion. Curr. Genet. 11: 553-564. (13) Jansen, R. K. and J. D. Palmer. 1987. A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc. Natl. Acad. Sci. USA 84: 5818-5822. (14) Jansen, R. K. and J. D. Palmer. 1988. Phylogenetic implications of chloroplast

12 DNA restriction site variation in the Mutisieae (Asteraceae). Amer. J. Bot. 75:751-764. (15) Steele, K. P., K. E. Holsinger, R. K. Jansen, and D. W. Taylor. 1988. Phylogenetic relationships in green plants - A comment on the use of 5S ribosomal RNA sequences by Bremer et al. Taxon 37: 135-138. (16) Palmer, J. D., R. K. Jansen, H. Michaels, J. Manhart, and M. Chase. 1988. Chloroplast DNA variation and plant phylogeny. Ann. Missouri Bot. Gard. 75: 1180-1206. (17) Jansen, R. K., J. D. Palmer, and H. J. Michaels. 1988. Investigations of chloroplast DNA variation in the Asteraceae. Compositae Newsletter 15: 2-9. (18) Schilling, E. E. and R. K. Jansen. 1989. Restriction fragment analysis of chloroplast DNA and the systematics of Viguiera and related genera (Asteraceae: Heliantheae). Amer. J. Bot. 76:1769-1778. (19) Olmstead, R. G., R. K. Jansen, H. J. Michaels, S. R. Downie, and J. D. Palmer. 1990. Chloroplast DNA and phylogenetic studies in the Asteridae. In: Biological Approaches and Evolutionary Trends in Plants. 4th International Symposium of Plant Biosystematics. Academic Press, New York, Pp. 119-134. (20) Jansen, R. K., K. E. Holsinger, H. J. Michaels, and J. D. Palmer. 1990. Phylogenetic analysis of chloroplast DNA restriction site data: an example from the Asteraceae. Evolution 44: 2089-2105. (21) Wallace, R. S. and R. K. Jansen. 1990. Systematic and evolutionary implications of chloroplast DNA variation in the genus Microseris D. Don (Asteraceae: Lactuceae). Syst. Bot. 15: 606-616. (22) Jansen, R. K., H. J. Michaels, and J. D. Palmer. 1991. Phylogeny and character evolution in the Asteraceae based on chloroplast DNA restriction site mapping. Syst. Bot. 16: 98-115. (23) Steele, K., K. E. Holsinger, R. K. Jansen and D. Taylor. 1991. Assessing the reliability of 5S rRNA sequence data for phylogenetic analysis in green plants. Mol. Biol. Evol. 8: 240-248. (24) Jansen, R. K., H. J. Michaels, R. S. Wallace, K.-J. Kim, S. C. Keeley, L. E. Watson, and J. D. Palmer. 1991. Chloroplast DNA variation in the Asteraceae: Phylogenetic and evolutionary implications. In: Molecular Systematics of Plants (eds. D. Soltis, P. Soltis, and J. Doyle). Chapman and Hall, New York, Pp. 252- 279. (25) Keeley, S. C. and R. K. Jansen. 1991. Evidence from chloroplast DNA for the recognition of a new tribe the Tarchonantheae, and the tribal placement of Pluchea (Asteraceae). Syst. Bot. 16: 173-181. (26) Bremer, B. B. and R. K. Jansen. 1991. Comparative restriction site mapping of chloroplast DNA implies new phylogenetic relationships within Rubiaceae. Amer. J. Bot. 78: 198-213. (27) Jansen, R. K., R. S. Wallace, K.-J. Kim, and K. L. Chambers. 1991. Systematic implications of chloroplast DNA variation in the subtribe Microseridinae (Asteraceae: Lactuceae). Amer. J. Bot. 78: 1015-1027. (28) Watson, L. E., R. K. Jansen, and J. Estes. 1991. Tribal placement of Marshallia (Asteraceae) based on evidence from chloroplast DNA restriction site mapping. Amer. J. Bot. 78: 1028-1035. (29) Philbrick, C. T. and R. K. Jansen. 1991. Phylogenetic studies of North American Callitrichaceae using chloroplast DNA restriction fragment analysis. Syst. Bot. 16: 478-491.

13 (30) Johansson, J. and R. K. Jansen. 1991. Chloroplast DNA variation among five species of Ranunculaceae: structure, sequence divergence and phylogenetic relationships. Plt. Syst. Evol. 178:9-25. (31) Raubeson, L. A. and R. K. Jansen. 1992. A rare chloroplast-DNA structural mutation is shared by all conifers. Biochem. Syst. Ecol. 20:17-24. (32) Raubeson, L. A. and R. K. Jansen. 1992. Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255:1697-1699. (33) Kim, K.-J., B. L. Turner, and R. K. Jansen. 1992. Phylogenetic and evolutionary implications of interspecific chloroplast DNA variation in dwarf dandelions (Krigia - Lactuceae - Asteraceae). Syst. Bot. 17:449-469. (34) Kim, K.-J., R. K. Jansen, R. S. Wallace, H. J. Michaels, and J. D. Palmer. 1992. Phylogenetic implications of rbcL sequence variation in the Asteraceae. Ann. Missouri Bot. Gard. 79: 428-445. (35) Kim, K.-J., R. K. Jansen, and B. L. Turner. 1992. Evolutionary implications of intraspecific chloroplast DNA variation in dwarf dandelions (Krigia-Asteraceae). Amer. J. Bot. 79:708-715. (36) Bremer, K., R. K. Jansen, P. O. Karis, and K.-J. Kim. 1992. Current research on Asteraceae phylogeny and classification. Compositae Newsl. 20/21:1-3. (37) Bremer, K. and R. K. Jansen. 1992. A new subfamily of Asteraceae. Ann. Missouri Bot. Gard. 79:414-415. (38) Bremer, K., R. K. Jansen, P. O. Karis, M. Kallerjso, S. C. Keeley, K.-J. Kim, H. J. Michaels, J. D. Palmer, and R. S. Wallace. 1992. A review of the phylogeny and classification of the Asteraceae. Nord. J. Bot. 12:141-148. (39) Capossela, A., J. A. Silander, R. K. Jansen, B. Bergen, and D. R. Talbot. 1992. Nuclear ribosomal DNA variation among ramets and genets of white clover. Evolution 46:1240-1247. (40) Spooner, D. M., G. J. Anderson, and R. K. Jansen. 1993. Chloroplast DNA evidence for the interrelationships of Tomatoes, Potatoes, and Pepinos. Amer. J. Bot. 80:676-688. (41) Michaels, H. J, K. M. Scott, R. O. Olmstead, T. Szaro, R. K. Jansen, and J. D. Palmer. 1993. Interfamilial relationships of the Asteraceae: Insights from rbcL sequence variation. Ann. Missouri Bot. Gard., 80: 742-751. (42) Chase, M., D. Soltis, R. Olmstead, D. Morgan, D. Les, B. Mishler, M. Duvall, R. Price, H. Hills, Y.-L. Qui, K. Kron, J. Rettig, E. Conti, J. Palmer, J. Manhart, K. Sytsma, H. Michaels, J. Kress, K. Karol, D. Clark, M. Hedren, B. Gaut, R. K. Jansen, K.-J. Kim, C. Wimpee, J. Smith, G. Furnier, S. Straus, Q.-Y. Xiang, G. Plunkett, P. Soltis, S. Swensen, S. Williams, P.Gadek, C. Quinn, L. Equiarte, E. Golenberg, G. Learn, Jr., S. Graham, S. Barrett, S. Dayanandan, and V. Albert. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Gard. 80: 528-580. (43) Johansson, J. T. and R. K. Jansen. 1993. Chloroplast DNA variation and phylogeny of the Ranunculaceae. Plt. Syst. Evol. 187:29-49. (44) Holsinger, K. E. and R. K. Jansen. 1993. Phylogenetic analysis of restriction site data. Meth. Enzy. 224:439-455. (45) Kim, K.-J. and R. K. Jansen. 1994. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia): additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Plt. Syst. Evol. 190: 157-185. (46) Cosner, M. B., R. K. Jansen, and T. G. Lammers. 1994. Phylogenetic relationships

14 in the Campanulales based on rbcL sequences. Plt. Syst. Evol. 190:79-95. (47) Mason, R. J., K. E. Holsinger, and R. K. Jansen. 1994. Biparental inheritance of the chloroplast genome in Coreopsis grandiflora (Asteraceae). J. Hered. 85:171-173. (48) Mione, T., R. O. Olmstead, R. K. Jansen, G. A. Anderson. 1994. Systematic implications of chloroplast DNA variation in Jaltomata and selected physaloid genera (Solanaceae). Amer. J. Bot. 81:912-918. (49) Kim, Y.-D. and R. K. Jansen. 1994. Characterization and phylogenetic distribution of a chloroplast DNA rearrangement in the Berberidaceae. Plt. Syst. Evol. 190:157-185. (50) Keeley, S.C. and R. K. Jansen. 1994. Chloroplast DNA restriction site variation in the Vernonieae (Asteraceae), an initial appraisal of the relationship of New and Old World taxa and the monophyly of Vernonia. Plt. Syst. Evol. 193:249-265. (51) Urbatsch, L. and R. K. Jansen. 1995. Phylogenetic affinities among and within coneflower genera (Asteraceae, Heliantheae), a chloroplast DNA analysis. Syst. Bot. 20:28-39. (52) Hempel, A. P. Reeves, R. Olmstead, and R. K. Jansen. 1995. Implications of rbcL sequence data for higher level relationships of the Loasaceae. Plt. Syst. Evol. 194:25-37. (53) Whitton, J., R. S. Wallace, and R. K. Jansen. 1995. Phylogenetic relationships and patterns of character change in the tribe Lactuceae (Asteraceae) based on chloroplast DNA restriction site variation. Can. J. Bot. 73:1058-1073. (54) Mason-Gamer, R., K. E. Holsinger, and R. K. Jansen. 1995. Chloroplast DNA haplotype variation within and among populations of Coreopsis grandiflora (Asteraceae). Mol. Biol. Evol. 12:371-381. (55) Wen, J. and R. K. Jansen. 1995. Morphological and molecular comparisons of Campsis grandiflora and C. radicans (Bignoniaceae), an eastern Asian and eastern North American vicariant species pair. Plt. Syst. Evol. 196: 173-183. (56) Bain, J. and R. K. Jansen. 1995. A phylogenetic analysis of the aureoid Senecio complex based on ITS sequence data. Plt. Syst. Evol. 195: 209-219. (57) Francisco-Ortega, J., R. K. Jansen, D. J. Crawford, and A. Santos-Guerra. 1995. Chloroplast DNA evidence for intergeneric relationships of the Macaronesian endemic genus Argyranthemum (Asteraceae). Syst. Bot. 20: 413-422. (58) Kim, K.-J. and R. K. Jansen. 1995. ndhF sequence evolution and the major clades in the sunflower family. Proc. Natl. Acad. Sci. USA 92: 10379-10383. (59) Wallace, R. S. and R. K. Jansen. 1995. DNA evidence for multiple origins of intergeneric allopolyploids in annual Microseris (Asteraceae). Plt. Syst. Evol. 198: 253-265. (60) Kim, Y.-D. and R. K. Jansen. 1995. Phylogenetic relationships of chloroplast DNA variation in the Berberidaceae. Plt. Syst. Evol.[Suppl.] 9: 341-349. (61) Levin, D. A., J. Francisco-Ortega, and R. K. Jansen. 1996. Hybridization and the extinction of rare plant species. Conserv. Biol. 10: 1-7. (62) Francisco-Ortega, J., R. K. Jansen and A. Santos-Guerra. 1996. Chloroplast DNA evidence of colonization, adaptive radiation, and hybridization in the evolution of the Macaronesian flora. Proc. Natl. Acad. Sci. USA 93: 4085-4090. (63) Loockerman, D. and R. K. Jansen. 1996. The use of herbarium material for molecular systematic studies. In: Sampling the Green World (ed. T. F. Stuessy and S. Sohmer), pp. 205-220. Columbia University Press. (64) Francisco-Ortega, J., R. K. Jansen, R. Mason, and R. S. Wallace. 1996. Application of chloroplast DNA restriction site studies for conservation genetics. In:

15 Molecular Genetic Approaches in Conservation (eds. T.B. Smith and R. Wayne), pp. 183-201. Oxford University Press, London. (65) Jansen, R. K. and K.-J. Kim. 1996. Implications of chloroplast DNA data for the classification and phylogeny of the Asteraceae. In, Proceedings of Compositae Symposium (eds. N. Hind, H. Beentje, and G. Pope), pp. 317-339. Royal Botanic Gardens, Kew, England. (66) Wen, J., R. K. Jansen, and E. A. Zimmer. 1996. Phylogenetic relationships and DNA sequence divergence of eastern Asian and eastern North American disjunct plants. In, Proceedings of the U.S.-Japan Binational Workshop on Molecular Evolution (M. Nei and N. Takahata, eds.), Hayama, Japan, pp. 37-44. (67) Lane, M. A., D. R. Morgan, Y. Suh, R. K. Jansen, and B. B. Simpson. 1996. Relationships of North American genera of Astereae based on chloroplast DNA restriction site data. In, Proceedings of Compositae Symposium (eds. N. Hind, H. Beentje, and G. Pope), 49-77. Royal Botanic Gardens, Kew, England. (68) Kim, Y.-D. and R. K. Jansen. 1996. Phylogenetic Implications of rbcL and ITS sequence variation in the Berberidaceae. Syst. Bot. 21:381-396. (69) Anderson, G. J., R. K. Jansen, and Y.-D. Kim. 1996. The origin and relationships of the 'pepino', Solanum muricatum (Solanaceae): DNA restriction fragment evidence. Econ. Bot. 50: 369-380. (70) Bain, J. F. and R. K. Jansen. 1996. Numerous chloroplast DNA polymorphisms are shared among different populations and species in the aureoid Senecio (Packera) complex. Canad. J. Bot. 74: 1719-1728. (71) Kim, S.-C., D. J. Crawford, and R. K. Jansen. 1996. Phylogenetic relationships among the genera of the subtribe Sonchinae (Asteraceae): Evidence from ITS sequences. Syst. Bot. 21: 417-432. (72) Panero, J. L. and R. K. Jansen. 1997. Chloroplast DNA restriction site study of Verbesina (Asteraceae: Heliantheae). Amer. J. Bot. 84: 382-392. (73) Wen, J., R. K. Jansen, and K. Kilgure. 1997. Evolution of the eastern Asian and eastern North American disjunct genus Symplocarpus (Araceae): insights from chloroplast DNA restriction site data. Biochem. Syst. Ecol. 24: 735-747. (74) Cosner, M. E., R. K. Jansen, J. D. Palmer, and S. R. Downie. 1997. The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr. Gen. 31: 419-429. (75) Francisco-Ortega, J., D. J. Crawford, A. Santos-Guerra, and R. K. Jansen. 1997. Origin and evolution of Argyranthemum (Asteraceae: Anthemideae) in Macaronesia. In T. J. Givnish and K. J. Sytsma (eds.) Molecular Evolution and Adaptive Radiation. Cambridge Univ. Press, London, pp 407-431. (76) Francisco-Ortega, J., A. Santos-Guerra, A. Hines, and R. K. Jansen. 1997. Molecular evidence for a Mediterranean origin of Argyranthemum (Asteraceae). Amer. J. Bot. 84: 1595-1613. (77) Wen, J., R. K. Jansen, and E. A. Zimmer. 1998. Phylogeny and Biogeography of Aralia sect. Aralia (Araliaceae). Amer. J. Bot. , 85: 866-875. (78) Prather, L. A. and R. K. Jansen. 1998. The phylogeny of Cobaea (Polemoniaceae) based on sequence data from the ITS region of nuclear ribosomal DNA. Syst. Bot., 23: 57-72. (79) Bierner, M. W. and R. K. Jansen. 1998. Systematic implications of DNA restriction site variation in Hymenoxys sensu lato (Asteraceae, Helenieae, Gaillardiinae). Lundellia 1: 17-26.

16 (80) Jansen, R. K., J. L. Wee, and D. Millie. 1998. Comparative utility of restriction site and DNA sequence data for phylogenetic studies in plants. In D. Soltis, P. Soltis, and J. Doyle (eds.), Molecular Systematics of Plants, 2nd edition. Chapman and Hall, New York, pp. 87-100. (81) Kim, K.-J. and R. K. Jansen. 1998. Chloroplast DNA phylogeny of lilacs (Syringa - Oleaceae): Plastome groups show a strong correlation with crossing groups. Amer. J. Bot. 85: 1338-1351. (82) Anderson, G. J. and R. K. Jansen. 1998. Biosystematic and molecular studies of Solanum section Basarthrum and the origin and relationships of the pepino dulce (S. muricatum). Pp. 17-32 in R. Fortunato and J. Bacigalupo (eds.), Proceedings of the VI Congreso Latinoamericano de Botánica, Missouri Botanical Garden Press, St. Louis, MO. (83) Kim, H.-G., S. C. Keeley, P. S. Vroom, and R. K. Jansen. 1998. Molecular evidence for an African origin of the Hawaiian endemic Hesperomannia (Asteraceae). Proc. Natl. Acad. Sci. USA, 95: 15440-15445. (84) Kim, Y-D. and R. K. Jansen. 1998. Chloroplast DNA restriction site variation and phylogeny of the Berberidaceae. Amer. J. Bot. 85: 1766-1778. (85) Jansen, R. K., D. J. Loockerman, and H.-G. Kim. 1999. DNA sampling from herbarium material: a current perspective. Pp. 277 – 286 in D. Metsger (ed.), Managing the Modern Herbarium: An Interdisciplinary Approach. Peanut Butter Press, Vancouver , BC, Canada. (86) Kim, S.-C., D. J. Crawford, A. Santos-Guerra, and R. K. Jansen. 1999. The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribe Sonchinae (Asteraceae: Lactuceae). Plt. Syst. Evol. 215: 85-99. (87) Francisco-Ortega, J., J. Fuertes-Aguilar, C. Gomez-Campo, A. Santos-Guerra, and R. K. Jansen. 1999. ITS sequence phylogeny of Crambe L. (Brassicaceae): Molecular data reveal two Old World disjunctions. Molec. Phyl. Evol. 11: 361-380. (88) Panero, J., R. K. Jansen, and J. A. Clevinger. 1999. Phylogenetic relationships of subtribe Ecliptinae (Asteraceae: Heliantheae) based on chloroplast DNA restriction site data. Amer. J. Bot. 86: 413-427. (89) Kim, Y. D., J. Lee, Y. Suh, S. Lee, S.-H. Kim, and R. K. Jansen. 1999. Molecular evidence for the phylogenetic position of Hanabusaya asiatica (Campanulaceae), an endemic in Korea. J. Plt. Biol. 42: 168-173. (90) Francisco-Ortega, J., L.R. Goertzen, A. Santos-Guerra, A. Benabid, and R. K. Jansen. 1999. Molecular systematics of the Asteriscus alliance (Asteraceae, Inuleae) I: Evidence from the internal transcribed spacers of nuclear ribosomal DNA. Syst. Bot., 24: 249-266. (91) Bremer, B., R. K. Jansen, M. Backlund, H. Lantz, and K.-J. Kim. 1999. More characters or more taxa for a robust phylogeny - a case study from the coffee family (Rubiaceae). Syst. Biol. 48: 413-435. (92) Panero, J. L., J. Francisco-Ortega, R. K. Jansen, and A. Santos-Guerra. 1999. Molecular evidence for multiple origins of woodiness and a New World biogeographic connection of the Macaronesian Island endemic Pericallis (Asteraceae: Senecioneae). Proc. Natl. Acad. Sci. USA 96: 13886-13891. (93) Gould, K. R. and R. K. Jansen. 1999. Taxonomy, Phylogeny, and the origin of a Gulf Coast disjunction in the Coelostylis species complex of Spigelia (Loganiaceae). Lundellia 2: 1-13. (94) Ferguson, C. F., F. Kramer, and R. K. Jansen. 1999. Relationships of eastern North American Phlox (Polemoniaceae) based on ITS sequence data. Syst. Bot. 24: 616-

17 631. (95) Mason-Gamer, R., R. K. Jansen, and K. E. Holsinger. 1999. Chloroplast DNA restriction site analysis of Coreopsis nuecensoides and C. nuecensis (Asteraceae), a progenitor-derivative species pair. Plt. Syst. Evol.. 218: 5-12. (96) Ferguson, C. J., R. K. Jansen, and D. A. Levin. 1999. Natural hybridization between an outcrossing and a selfing species of Phlox: Insights from DNA restriction site variation. Plt. Syst. Evol. 218: 153-158. (97) Caujape-Castells, J., R. K. Jansen, J. Pedrola-Monfort, and N. Membrives. 1999. Chloroplast DNA restriction site phylogeny of the genus Androcymbium Willdenow (Colchicaceae). Syst. Bot.. 24: 581-597. (98) Helfgott, D. M., J. Francisco-Ortega, A. Santos-Guerra, R. K. Jansen, and B. B. Simpson. 2000. Molecular systematics of the Bencomia alliance (Rosaceae) in Macaronesia: evidence for a Mediterranean origin. Syst. Bot. 25: 82-97. (99) Linder, C. R., L. R. Goertzen, B. Vanden Heuvel, J. Francisco-Ortega, and R. K. Jansen. 2000. The external transcribed spacer of the rDNA repeat: A new nuclear region for low-level taxonomic analyses of the Asteraceae and closely allied families. Mol. Phylogen. Evol. 14: 285-303 (100) Prather, L. A., C. J. Ferguson, and R. K. Jansen. 2000. Polemoniaceae phylogeny and classification: Implications of sequence data from the chloroplast gene ndhF. Amer. J. Bot. 87: 1300-1308.. (101) Olmstead, R. G., K.-J. Kim, R. K. Jansen, and S. J. Wagstaff. 2000. The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences. Mol. Phylogen. Evol. 16: 96-112. (102) Cosner, M.E, Jansen, R. K., Moret, B. M. E., Raubeson, L. A., Wang, L.-S., Warnow, T., and Wyman S. (2000). A new fast heuristic for computing the breakpoint phylogeny and experimental analyses of real and synthetic data. In “Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology,” (P.Bourne, M. Gribskov, R. Altman, N. Jensen, D. Hope, T. Lengauer, J. Mitchell, E. Scheeff, C. Smith, S. Strande, and H. Weissig, Eds.), pp. 104-115, La Jolla, CA, USA. (103) Cosner, M. E, Jansen, R. K., Moret, B.M.E., Raubeson, L. A., Wang, L.-S., Warnow, T., and Wyman, S. (2000). An empirical comparison of phylogenetic methods on chloroplast gene order in Campanulaceae. In “Comparative Genomics, Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families,” (D. Sankoff and J. H. Nadeau, Eds.), pp. 99-121. Kluwer Academic Publishers, Netherlands. (104) Barber, J. C., Javier Francisco-Ortega, A. Santos-Guerra, A. Marrero, and R. K. Jansen. 2000. Evolution of endemic Sideritis (Lamiaceae) in Macaronesia: insights from a chloroplast DNA restriction site analysis. Syst. Bot., 25: 633-647. (105) Zhao, Z., J. Skvarla, R. K. Jansen, and M. L. Devore. 2000. Phylogenetic implications of pollen morphology and ultrastructure in the Barnadesiodeae (Asteraceae). Lundellia 3: 26-40. (106) DeVore, M. L., Z. Zhao, R. K. Jansen, and J. Skvarla. 2000. Utility of trends in pollen morphology for phylogenetic analyses: An example using subfamilies Barnadesioideae and Cichorioideae (Asteraceae). Proceedings of Pollen and Spores 1998: Morphology and Biology. (107) Francisco-J., J. C. Barber, A. Santos-Guerra, R. Febbles-Hernandez, and R. K. Jansen. 2001. Origin and evolution of the endemic genera of Gonosperminae (Asteraceae: Anthemideae) from the Canary Islands: Evidence from nucleotide

18 sequences of the internal transcribed spacers of the nuclear ribosomal repeat. Amer. J. Bot. 88: 161-169. (108) Park, S.-J., E. Korompai., J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen. 2001. Phylogenetic relationships of Tolpis (Asteraceae: Lactuceae) based on ndhF sequence data. Plt. Syst. Evol. 226: 23-33. (109) Francisco-J., J., S.-J. Park, A. Santos-Guerra, A. Benabid, and R. K. Jansen. 2001. Origin and evolution of the endemic Macaronesian Inuleae (Asteraceae): Evidence from the internal transcribed spacers of nuclear ribosomal DNA. Biol. J. Linn. Soc. 72: 77-97. (110) Caujapé-Castells, J., R. K. Jansen, N. Membrives, J. Pedrola-Monfort, J. M. Montserrat, and A. Ardanuy. 2001. Historical biogeography of Androcymbium Willd. (Colchicaceae) in Africa: evidence from cpDNA RFLPs. Bot. J. Linn. Soc., 136: 379 - 392. (111) Goldman, D. H., J. V. Freudenstein, P. J. Kores, M. Molvray, D. D. Jarrell, M. W. Whitten, K. M. Cameron, R. K. Jansen, and M. W. Chase. 2001. Phylogenetics of Arethuseae (Orchidaceae) based on plastid matK and rbcL sequences. Syst. Bot. 26: 670-695. (112) Jansen, R.K 2001. Treatments of Acmella and tribe Lactuceae for the Flora of Nicaragua, Missouri Botanical Garden. (113) Furetes-Aguilar, J., M. C. Ray, J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen. 2002. Molecular evidence from chloroplast and nuclear markers for multiple colonizations of Lavatera (Malvaceae) in the Canary Islands. Syst. Bot.27:74-83. (114) Moore, M. J., J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen. 2002. Chloroplast DNA evidence for the roles of island colonization and extinction in Tolpis (Asteraceae: Lactuceae). Amer. J. Bot. 89: 518-526. (115) Wang, L.-S., R, K. Jansen, B. M. E. Moret, L. A. Raubeson, and T. Warnow. 2002. Fast phylogenetic methods for analysis of genome rearrangement data: An empirical study. In Proc., 7th Pacific Symp. Biocomputing PSB 2002. (116) Caujapé-Castells, J., R. K. Jansen, N. Membrives, J. Pedrola-Monfort. 2002. Space- time diversification of Androcymbium Willd. (Colchicaceae) in western South Africa. Plt. Syst. Evol. 232: 73-88. (117) Barber, J. C., J. Francisco-Ortega, A. Santos-Guerra, K. G. Turner, and R. K. Jansen. 2002. Origin of Macaronesian Sideritis L. (Lamioideae: Lamiaceae) inferred from nuclear and chloroplast sequence datasets. Mol. Phyl. Evol. 23: 293- 306. (118) Ferguson, C. J. and R. K. Jansen. 2002. A chloroplast DNA phylogeny or eastern Phlox (Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny. Amer. J. Bot. 89: 1324-1335. (119) Kim, H.-G., D. J. Loockerman, and R. K. Jansen. 2002. Systematic implications of ndhF sequence variation in the Mutisieae (Asteraceae). Syst. Bot. 27: 598-609. (120) Goertzen, L. G., J. Francisco-Ortega, A. Santos-Guerra, J. Mower, C. R. Linder, and R. K. Jansen. 2002. Molecular systematics of the Asteriscus alliance (Asteraceae: Inuleae) II: Combined nuclear and chloroplast data. Syst. Bot. 27:815-823. (121) Francisco-Ortega, J., J. Furetes-Aguilar, Kim, S.-C., A. Santos-Guerra, D. J. Crawford, and R. K. Jansen. 2002. Phylogeny of the Macaronesian endemic Crambe section Dendrocrambe (Brassicaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA. Amer. J. Bot., 89 (12): 1984-1990.

19 (122) Fuertes-Aguilar, J., P. A. Fryxell, and R. K. Jansen. 2003. Phylogenetic relationships and classification of the Sida generic alliance (Malvaceae) based on nrDNA ITS evidence. Syst. Bot. 28: 352-364. (123) Loockerman, D. L., B. L. Turner, and R. K. Jansen. 2003. Phylogenetic relationships within the Tageteae (Asteraceae) based on nuclear ribosomal ITS and chloroplast ndhF gene sequences. Syst. Bot. 28: 191-207. (124) Caujape-Castells, J. and R. K. Jansen. 2003. The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae). Mol. Ecol. 12: 1515- 1525. (125) Goertzen, L. R., J. J. Cannone, R. R. Gutell, and R. K. Jansen. 2003. ITS secondary structure derived from comparative analysis: Implications for sequence alignment and phylogeny of the Asteraceae. Mol. Phylog. Evol. 29:216-234. (126) Eddie, W. M. M, T. Shulkina, J. Gaskin, R. C. Haberle, and R. K. Jansen. 2003. Phylogeny of the Campanulaceae s. str. inferred from ITS sequences of nuclear ribosomal DNA. Ann. Missouri Bot. Gard. 90: 554-575. (127) Kim, Y.-D., S.-H. Kim, and R. K. Jansen. 2004. Phylogeny of the Berberidaceae based on sequences of the chloroplast gene ndhF. Biochem. Syst. Ecol., 32: 291-302. (128) Andrus, N., J. Trusty, A. Santos-Guerra, R. K. Jansen and J. Francisco-Ortega. 2004. Using molecular phylogenies to test phytogeographical links between East/South Africa – Southern Arabia and the Macaronesian islands – A review and the case of Pulicaria section Vieraeopsis and Vierea (Asteraceae). Taxon 53: 333 - 346. (129) Goldman, D.H., C. van den Berg, R.K. Jansen, I.J. Leitch, M.F. Fay, and M.W. Chase. 2004. Molecular and cytological examination of Calopogon (Orchidaceae, Epidendroideae): circumscription, phylogeny, polyploidy, and potential hybrid speciation. Amer. J. Bot. 91:707-723. (130) Cosner, M.E., L. A. Raubeson, and R. K. Jansen. 2004. Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evolutionary Biology 4: 27. (131) Wyman, S. K., J. L. Boore, and R. K. Jansen. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252 - 3255. (132) Raubeson. L.A. and R. K. Jansen. 2005. Chloroplast genomes of plants. In, Diversity and Evolution of Plants - Genotypic and Phenotypic Variation in Higher Plants (ed., R. Henry). CABI Publishing, UK. Pp. 45-68. (133) Jansen, R.K., L. A. Raubeson, J. L. Boore, C. W. dePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman, A. J. Alverson, R. Peery, S. J. Herman, H. M. Fourcade, J. V. Kuehl, J. R. McNeal, J. Leebens-Mack, and L. Cui. 2005. Methods for obtaining and analyzing chloroplast genome sequences. Methods in Enzymology 395: 348 - 384. (134) Funk, V. A., R. J. Bayer, S. Keeley, R. Chan, L. Watson, B. Gemeinholzer, E. Schilling, J. L. Panero, B. G. Baldwin, N. Garcia-Jacas, A. Susanna and R. K. Jansen. 2005. Everywhere but Antarctica: Using a supertree to understand the diversity and distribution of the Compositae. Biol. Skr. 55: 343-374. (135) Kim, K.-J., K.-S. Choi, and R. K. Jansen. 2005. Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Molecular Biology and Evolution 22: 1783-1792. (136) Leebens-Mack, J., L. A. Raubeson, L. Cui, J. Kuehl, M. Fourcade, T. Chumley, J. L. Boore, R. K. Jansen, and C. W. dePamphilis. 2005. Identifying the basal

20 angiosperms in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone. Molecular Biology and Evolution 22: 1948-1963. (137) Ganapathy, G., B. Goodson, R. K. Jansen, V. Ramachandran, and T. Warnow. 2005. Pattern identification in biogeography. 5th Workshop on Algorithms in Bioinformatics. R. Casadio and G. Myers (Eds.): WABI 2005, LNBI 3692, pp. 116– 127, 2005. Springer- Berlin Heidelberg 2005. (138) Saski, C., S. Lee, H. Daniell, T. Wood, J. Tomkins, H.-G. Kim, and R. K. Jansen. 2005. Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Molecular Biology 59:309-322. (139) Hansen, A. K., L. E. Gilbert, B. B. Simpson, S. R. Downie, A. C. Cervi, and R. K. Jansen. 2006. Phylogenetic relationships and chromosome evolution in tropical Passiflora based on cpDNA trnL/trnT intergenic spacer sequences and distribution of the chloroplast rpoC1 intron. Systematic Botany 31: 138-150. (140) Cui, L., Veeraraghavan, N. Wall, K., Jansen, R.K., Leebens-Mack, Jim, Makalowska, I., dePamphilis, C. W. 2006. ChloroplastDB: the chloroplast genome database. Nucleic Acids Research 34:D692-D696. (141) Jansen, R.K., C. Kaittanis, C. Saski, S-B. Lee, J. Tompkins, A. J. Alverson, and, H. Daniell. 2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: Effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evolutionary Biology 6: 32. (142) Lee, S.-B., Kaittanis, C.,J., Hostetler, C. Town, R. K. Jansen, and H. Daniell. 2006. The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7: 61. (143) Daniell, H., S.-B. Lee, J. Grevich, C. Saski, C. Guda, J. Tompkins, and R. K. Jansen. 2006. Complete chloroplast genome sequences of Solanum tuberosum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theoretical and Applied Genetics 112: 1503-1518. (144) Moore, M. J. and R. K. Jansen. 2006. Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae). Molecular Phylogenetics and Evolution 39: 668-687. (145) Bain, J.F. and R.K. Jansen. 2006. A chloroplast DNA hairpin structure provides useful phylogenetic data with subtribe Senecioneae (Asteraceae). Canadian Journal of Botany 84:862-868. (146) Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, Depamphilis C, Desalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. 2006. Taking the first steps towards a standard for reporting on phylogenies: Minimal information about a phylogenetic analysis (MIAPA). OMICS: A Journal of Integrative Biology10: 231-237. (147) Moore, M. J., A. Tye, and R. K. Jansen. 2006. Patterns of long-distance dispersal in Tiquilia subg. Tiquilia (Boraginaceae): Implications for the origins of amphitropical disjuncts and Galapogos island endemics. American Journal of Botany 93: 1163-1177. (148) Ruhlman, T., S.-B. Lee, R. K. Jansen, J. B. Hostetler, L. J. Tallon, C. D. Town, and H. Daniell. 2006. Complete chloroplast genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7: 222.

21 (149) Chumley, T. W., J. D. Palmer, J. P. Mower, J. L. Boore, H. M. Fourcade, P. J. Caile, and R. K. Jansen. 2006. The complete chloroplast genome sequence of Pelargonium x hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution 23: 1-16. (150) Bausher, M. G., N. D. Singh, S.-B. Lee, R. K. Jansen, and H. Daniell. 2006. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var. 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biology 6:21. (151) Zhao, Z, J. J. Skvarla, and R. K. Jansen. 2006. Mutisieae (Asteraceae) pollen ultrastructure atlas. Lundellia 9: 51-76. (152) Goodson, B.E., A. Santos-Guerra, and R. K. Jansen. 2006. Molecular systematics of Descurainia (Brassicaceae) in the Canary Islands: biogeographic and taxonomic implications. Taxon 55: 671-682. (153) Cai, Z., C. Penaflor, J.V. Kuehl, J. Leebens-Mack, J. Carlson, C.W. dePamphilis, and R.K. Jansen. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: Implications for the phylogeny of magnoliids. BMC Evolutionary Biology 6:77. (154) Wang, L.-S., T. Warnow, B.M.E. Moret, and R.K. Jansen. 2006. Distance-based genome rearrangement phylogeny. 2006. Journal of Molecular Evolution 63 (4): 473-483. (155) Ganapathy, G., B. Goodson, R. K. Jansen, H.-S. Le, V. Ramachandran, and T. Warnow. 2006. Pattern identification in biogeography. IEEE/ACM Transactions on Computational Biology and Bioinformatics (invited paper) 3 (4): 334-346. (156) Hansen, A. K., L. E. Escobar, L. E. Gilbert, and R. K. Jansen. 2007. Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): Implications for phylogenetic studies. American Journal of Botany 94: 42-46. (157) Samson, N., M.G. Bausher, S.B. Lee, R. K. Jansen, and H. Daniell. 2007. The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for bioengineering and phylogenetic relationships among angiosperms. Plant Biotechnology Journal 5: 339-353. (158) Timme, R. E., J. V. Kuehl, J. L. Boore, and R. K. Jansen. 2007. A comparison of the first two sequenced chloroplast genomes in Asteraceae: Lettuce and Sunflower. American Journal of Botany 94: 302-312. (159) Barber, J.C., C.C. Finch, J. Francisco-Ortega, A. Santos-Guerra, and R. K. Jansen. 2007. Evolution of Macaronesian Sideritis (Lamiaceae) revisited: A re-evaluation based upon incongruence of multiple independent nuclear and chloroplast datasets. Taxon 56: 74-88. (160) Moore, M.J. and R. K. Jansen. 2007. The origins and biogeography of obligate gypsophily in the Chihuahuan desert plant group Tiquilia subg. Eddya (Boraginaceae). Systematic Botany 32: 392-414. (161) Lee, H-L., R. K. Jansen, T.W. Chumley, and K-J. Kim. 2007. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Molecular Biology and Evolution 24: 1161-1180. (162) Saski, C., S.-B. Lee, S. Fjellheim, C. Guda, R. K. Jansen, H. Luo, J. Tomkins, O. A. Rognli, H. Daniell, and J. L. Clarke. 2007. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera and

22 comparative analyses with other grass genomes. Theoretical and Applied Genetics 115:571-590. (163) Raubeson, L.A., R. Peery, T. Chumley, Dziubek, C., H. M. Fourcade, J. L. Boore, and R. K. Jansen. 2007. Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8:174. (164) Alverson, A.J., R. K. Jansen, and E. C. Theriot. 2007. Bridging the Rubicon: Phylogenetic Analysis Reveals Repeated Colonizations of Marine and Fresh Waters by Thalassiosiroid Diatoms. Molecular Phylogenetics and Evolution 45:193- 210. (165) DeVore, M.L., Zhao, Z., Jansen, R.K., and Skvarla, J.J. 2007. Phylogenetic implications of pollen ultrastructure in the Calyceraceae. Lundellia 10:32-48. (166) Hansen, D.R., S.G., Dastidar, Z.Cai, C. Penaflor, J.V. Kuehl, J.L. Boore, and R. K. Jansen. 2007. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Molecular Phylogenetics and Evolution 45:547-563. (167) Jansen, R. K., Cai, Z., Raubeson, L.A., Daniell, H., dePamphilis, C.W., Leebens- Mack, J., Müller, K.F., Guisinger-Bellian, M., Haberle, R.C., Hansen, A.K., Chumley, T.W., Lee, S.-B., Peery, R., McNeal, J., Kuehl, J.V., and Boore, J.L. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences USA 104: 19369-19374. (168) Park, K.-R. and Jansen, R.K. 2007. A phylogeny of Euphorbieae subtribe Euphorbiinae (Euphorbiaceae) based on molecular data. Journal of Plant Biology 50: 644-649. (169) Daniell, H. Wurdack, K.J., Kanagaraj, A., Lee, S-B., Saski, C., and Jansen, R. K. 2008. The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and multiple losses of the atpF intron in Malpighiales. Theoretical and Applied Genetics 116: 723-737. (170) Haberle, R. C., M. L. Fourcade, J. L. Boore, and R. K. Jansen. 2008. Complete chloroplast genome of Trachelium caeruleum: extensive rearrangements are associated with repeats and tRNAs. Journal of Molecular Evolution 66: 350-361. (171) Steele, P.R., M. Guisinger-Bellian, C. R. Linder, and R. K. Jansen. 2008. Phylogenetic utility of 144 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids. Molecular Phylogenetics and Evolution 48:1013-1026. (172) Jansen, R.K., Wojciechowski, M.F., E. Sanniyasi, S.-B. Lee, and H. Daniell. 2008. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Fabaceae). Molecular Phylogenetics and Evolution 48: 1204-1207. (173) Guisinger, M., J.V. Kuehl, J.L. Boore, and R.K. Jansen. 2008. Genome-wide analyses of Geraniaceae plastid DNA reveal patterns of increased nonsynonymous substitutions. Proceedings of the National Academy of Sciences USA 105: 18424-18429. (174) Alverson, A.J., R.K. Jansen, and E.C. Theriot. 2008. Letter to the editor: Response to Medlin and Kaczmarska. Molecular Phylogenetics and Evolution 50: 407-408.

23 (175) Cai, Z., M. Guisinger, H.-G. Kim, E. Ruck, V. McMurtry, J.V. Kuehl, J.L. Boore, and R.K. Jansen. 2008. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. Journal of Molecular Evolution 67:6-14. (176) Haberle, R.S., A. Dang, T. Lee, C. Penaflor, H. Cortes-Burns, A. Oestreich, L. Raubeson, E. Edwards, S.-T. Tang, N. Cellinese, W.M.M. Eddie, and R.K. Jansen. 2009. Molecular systematics of Campanulaceae sensu stricto using chloroplast DNA sequences of atpB, matK, and rbcL. Taxon 58: 715–734. (177) Gruenstaeudl, M., E. Urtebey, R.K. Jansen, R. Samuel, M.H.J. Barfuss, and T.F. Stuessy. 2009. Phylogeny of Barnadesioideae (Asteraceae) based on DNA sequences of nuclear rDNA, nine chloroplast regions and morphology. Molecular Phylogenetics and Evolution 51: 572-587. (178) Guisinger, M.M., T.W. Chumley, J.V. Kuehl, J.L. Boore, and R.K. Jansen. 2010. Implications of the plastid genome sequence of Typha latifolia (Typhaceae, Poales) for understanding genome evolution in Poaceae. Journal of Molecular Evolution 70:149-166. (179) Steele, P.R., L.M. Friar, L.E. Gilbert, and R.K. Jansen. 2010. Molecular systematics of the neotropical genus Psiguria (Cucurbitaceae): Implications for phylogeny and species identification. American Journal of Botany 97: 156-173. (180) Theriot, E.C., M. Ashworth, E. Ruck, T. Nakov and R.K. Jansen. 2010. A preliminary multigene phylogeny of the diatoms (Bacillariophyta): Challenges for future research. Plant Ecology and Evolution 143:1-18. (181) Guisinger, M.M., Kuehl, J.V., Boore, J.L., and R.K. Jansen. 2011. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage. Molecular Biology and Evolution 28:583- 600. (182) Jansen, R.K., C. Saski, S.-B. Lee, A. K. Hansen, and Henry Daniell. 2011. Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Molecular Biology and Evolution 28:835-847. (183) Theriot E.C. Ashworth M, Ruck E., Nakov T., and R.K. Jansen. 2011. Status of the Pursuit of the diatom phylogeny: Are traditional views and new molecular paradigms really that different? Book Chapter for Cellular Origin, Life in Extreme Habitats and Astrobiology: The Diatom World. Springer Science. (184) Blazier J.C., Guisinger M.M., Jansen R.K. 2011. Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Molecular Biology 76:263-272. (185) Goodson, B.E., S.K. Rehman, and R.K. Jansen. 2011. Molecular systematics and biogeography of Descurainia (Brassicaceae) based on nuclear and non –coding chloroplast DNA. Systematic Botany 36: 1-24. (186) Jansen, R.K. and T.A. Ruhlman. 2012. Plastid genomes of seed plants. In: Advances in Photosynthesis and Respiration 35, Genomics of chloroplasts and mitochondria. Bock, R. and Knoop, V. (eds), Springer, Dordrecht Advances, pp. 103–126. (187) Weng M.-L., Ruhlman T.A., Gibby M., and R. K. Jansen. 2012. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). Molecular Phylogenetics and Evolution 64: 654-670.

24 (188) Gruenstaeudl M., Santos-Guerra A, Jansen RK. 2013. Phylogenetic analyses of Tolpis Adans. (Asteraceae) reveal patterns of adaptive radiation, multiple colonization, and interspecific hybridization. Cladistics 29: 416-434. (189) Alzohairy A.M., Gyulai G., Jansen R.K., Bahieldin A. 2013. Transposable elements domesticated and neofunctionalized by eukaryotic genomes. Plasmid 69: 1-15. (190) Gruenstaeudl M, Hawkes CW, Santos-Guerra A, Jansen RK. 2013. Preliminary investigations of correlated diversification between plants and their associated arbuscular mycorrhizal fungi in Macaronesia. Proceedings of the International Conferences on Island Biodiversity 2011. Jardín Botánico Canario “Viera y Clavijo”, ed. J Caujape-Castells, 9 pp. (191) Gruenstaeudl M, Santos-Guerra A, Hawkes CW, Jansen RK. 2013. Molecular survey of arbuscular mycorrhizal fungi associated with Tolpis (Asteraceae) on three Canarian islands. Vieraea 41: 199-218. (192) Sabir JS, Baeshen NA, Shokry AM, Gadalla NO, Edris S, Mutwakil MH, Ramadan AM, Atef A, Al-Kordy MA, Abuzinadah OA, El-Domyati FM, Jansen RK, Bahieldin A. 2013. Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly. C R Biologies 336: 521-529. (193) Zhang J, Ruhlman TA, Mower JP, Jansen RK. 2013. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing. BMC Plant Biology 13:228. (194) Sabir J.S.M., Abo-Aba S., Bafeel S., Zari T.A., Edris S., Shokry A.M., Atef A., Gadalla N.O., Ramadan A.M., Al-Kordy M.A., El-Domyati F.M., Jansen R.K. and Bahieldin A. 2014. Characterization of ten date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia using AFLP and ISSR markers. C R Biologies 337: 6–18. (195) Weng, M.-L., Blazier, J.C., Govindu, M., Jansen, R.K. 2013. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats and nucleotide substitution rates. Molecular Biology and Evolution 31: 645-659. (196) Ruhlman T.A. and R.K. Jansen. 2014. The plastid genomes of flowering plants. In: Chloroplast Biotechnology: Methods and Protocols, Maliga, P. (ed), Springer, Humana Press, pp. 3-38. (197) Alzohairy A.M., Sabir, J.S.M., Gyulai G., Younis, R.A., Jansen R.K., Bahieldin A. 2014. Environmental Stress Activation of Plant LTR-Retrotransposons. Functional Plant Biology 41: 557–567. (198) Alzohairy A.M., Gyulai G., Ramadan MA, Edris S, Sabir, J.S.M., Jansen R.K., Eissa HF, Bahieldin A. 2014. Retrotransposon-based molecular markers for assessment of genomic diversity. Functional Plant Biology 41: 781-789, http://dx.doi.org/10.1071/FP13351. (199) Sabir JSM, Schwarz E, Ellison N, Zhang J, Baeshen N, Mutwakil M, Jansen RK, Ruhlman TA. 2014. Evolutionary and biotechnology implications of plastid genome variation in the IR loss clade of legumes. Plant Biotechnology Journal 12: 743-754. (200) Ruck EC, Nakov T, Jansen RK, Theriot EC, Alverson AJ. 2014. Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms. Genome Biology and Evolution 6: 644-654, doi:10.1093/gbe/evu039. (201) Sabir JSM Arasappan D, Bahieldin A, Abo-Aba1 S, Bafeel , Zari TA, Edris S, Shokry AM, Gadalla NO, Ramadan MA, Atef A, Al-Kordy MA, El-Domyati FM, Jansen RK. 2014. Whole mitochondrial and plastid genome SNP analysis of nine

25 date palm cultivars reveals plastid heteroplasmy and relationships among cultivars. PloS One 9(4): e94158. doi:10.1371/journal.pone.0094158. (202) Park S, Ruhlman TA, Sabir JSM, Mutwakil MHZ, Baeshen MN, Sabir MJ, Baeshen NA, Jansen RK. 2014. Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids. BMC Genomics 15:405. (203) Bahieldin A., Al-Kordy M.A., Shokry AM , Gadalla NO, Al-Hejin A.M.M., Sabir JSM, Hassan S.M., Al-Ahmadi A.A., Schwarz E.N., El-Domyati1 F.M., Jansen R.K. 2014. Corrected sequence of the wheat plastid genome. C R Biologies 337: 727-731, doi : 10.1016/j.crvi.2014.07.001. (204) Sabir J.S.M., Yu M., Ashworth M.P., Baeshen N.A., X Baeshen M.N., Bahieldin A., Theriot E.C., and Jansen R.K. 2014. Conserved gene order and expanded inverted repeats characterize plastid genomes of Thalassiosirales. PloS One 9 (9) e107854. (205) Downie SR, Peery RM, and Jansen RK. 2015. Another first for the Apiaceae: evidence fir mitochondrial DNA transfer into the plastid genome. Journal of Faculty of Pharmacy of Istanbul University 44: 131-144. (206) Downie SR and Jansen RK. 2015. A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Systematic Botany 40: 336–351. (207) Park S., Jansen R.K., Park S-J. 2015. Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and the transfer of ribosomal protein L32 to the nucleus in the ancestor of the subfamily Thalictroideae. BMC Plant Biology 15:40. (208) Zhang J., Ruhlman T.A., Sabir J.S.M., Blazier J.C. and Jansen R.K. 2015. Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae. Plant Cell 27: 563-573. (209) Alzohairy A.M., Kalendar R, Gyulai G., Ramadan MA, Edris S, Sabir, J.S.M., Jansen R.K., Bahieldin A. 2014. Retrotransposon-based molecular markers for assessment of genomic diversity. Functional Plant Biology 41: 781-789. http://dx.doi.org/10.1071/FP13351 (210) Theriot E.C., Ashworth M., Nakov T., Ruck E., and Jansen R.K. 2015. Dissecting signal and noise in Diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution 89: 28-36. (211) Ruhlman T.A., Chang W.J., Chen J.J.W., Huang Y.-T., Chan M.-T., Zhang J., Liao D.-C., Blazier J.C., Jin X., Shih M.-C., Jansen R.K., and Lin C.-S. 2015. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC Plant Biology 15: 100. (212) Alzohairy A.M., Gyulai G., Mustafa M.M., Edris S., Sabir J.S.M., Jansen R.K., Tóth Z., Bahieldin A. 2015. Retrotransposon-based Plant DNA Barcoding. Plant DNA barcoding and phylogenetics, Edited by Ali MA, G Gyulai, F Al-Hemaid, 01/2015: chapter 6: pages 91-105; LAP Lambert Academic Publ. Germany., ISBN: ISBN-13: 978-3-659-28095-5. (213) Park S., Grewe F., Zhu A., Ruhlman T.A., Sabir H., Mower J.P., and Jansen R.K. 2015. Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers. New Phytologist 208: 570-583. DOI: 10.1111/nph.13467. (214) Bahieldin A., Sabir J.S.M., Atef A., Radwan N.A., Baeshen M.N., Ramadan A.M., Baeshen N.A., El-Domyatil F.M., and Jansen R.K. 2015. RNA-Seq analysis of the

26 wild barley (H. spontaneum) leaf transcriptome under salt stress. C R Biologies 338: 285–297. (215) Schwarz E., Ruhlman T.A., Sabir J.S.M., Hajrah N.H., Alharbi N.S., Al-Malki A.L., Bailey C.D. and Jansen R.K. 2015. Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids. Journal of Systematics and Evolution 53: 458-468. DOI: 10.1111/jse.12179. (216) Dugas D.V., Hernandez D., Koenen E., Schwarz E., Straub S., Hughes C.E., Jansen R.K., Nageswara-Rao M., Staats M., Trujillo J., Hajrah N.H., Alharbi N.S., Al-Malki A.L., Sabir J.S.M., and Bailey C.D. 2015. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Scientific Reports DOI: 10.1038/srep16958. (217) Li C.L., Ashworth M.P., Witkowski A., Dabek P., Medlin L.K., Kooistra W.H.C.F., Sato S., Zglobicka I., Kurzydlowski K.J., Theriot E.C., Sabir J.S.M., Khiyami M.A., Mutwakil M.H.Z., Sabir M.J., Alharbi N.S., Hajarah N.H., Qing S. and Jansen R.K. New insights into Plagiogrammaceae (Bacillariophyta) based on multigene phylogenies and morphological characteristics with the description of a new genus and three new species. PLoS ONE 10(10): e0139300. doi:10.1371/journal.pone.0139300. (218) Bromke M.A., Sabir J.S., Alfassi F.A., Abuzinadah O.A., Redwan N.A., Mutwakil M.Z., Ashworth M.P., Jansen R.K., and Wilmitzer L. 2015. Metabolomic profiling of 13 diatom cultures and their adaptation to nitrate-limited growth conditions. PLoS ONE 10 (10): e0138965. doi:10.1371/journal.pone.0138965. (219) Walker J.F., Jansen R.K., Zanis M.J. and Emery N.C. 2015. Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. American Journal of Botany 102: 1751-1752. (220) Witkowsk A.i, Li C., Zgłobicka I., Yu S-X., Ashworth M., Dąbek P., Qin S., Tang C., Krzywda M., Ruppel M., Theriot E.C., Jansen R.K., Car A., Płociński T., Wang Y- C., Sabir J.S.M., Daniszewska-Kowalczyk GT., Kierzek A. and Hajrah N.H. 2016. Multigene assessment of biodiversity of diatom (Bacillariophyceae) assemblages from the littoral zone of the Bohai and Yellow Seas in Yantai region of northeast China with some remarks on ubiquitous taxa. Journal of Coastal Research 74 (Special Issue): 164-193. (221) Zhang J., Ruhlman T.A., Sabir J.S.M., Blazier J.C., Weng M.-L., Park S., and Jansen R.K. 2016. Coevolution between nuclear encoded DNA replication, recombination and repair genes and plastid genome complexity. Genome Biology and Evolution 8: 622-634, doi:10.1093/gbe/evw033. (222) Blazier J.C., Ruhlman T.A., Weng M.-L., Rehman S.K., Sabir J.S.M., and Jansen R.K. 2016. Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement. Scientific Reports 6:24595, DOI: 10.1038/srep24595. (223) Blazier J.C., Jansen R.K., Mower J.P., Govindu M., Zhang J., Weng M.-L., and Ruhlman T.A. 2016. Variable presence of the inverted repeat and plastome stability in Erodium. Annals of Botany 117:1209-1220, doi:10.1093/aob/mcw065. (224) Weng M.-L., Ruhlman T.A. and Jansen R.K. 2016. Nonsynonymous substitutions in nuclear-encoded plastid targeted genes drive evolution of plastid-encoded genes in Geraniaceae. Genome Biology and Evolution 8:1824-1838, doi: 10.1093/gbe/evw115.

Manuscripts in Review

27

(225) Obaid A.Y., Sabir J.S.M., Atef A., Liu X., El-Domyati F.M., Mutwakil M.Z., Gadalla N.O., Hajrah N.H., Al-Kordy M.A., Hall N., Jansen R.K. and Bahieldin A. 2016. Analysis of transcriptional response to heat stress in Rhazya stricta. BMC Plant Biology, in review. (226) Peery R., Downie S.R., Ming R., Jansen R.K. amd Raubeson L.A. 2016. Inverted repeat changes and incorporation of novel DNA in Apiaceae plastomes are facilitated by double-strand break repair and short dispersed repeats. New Phytologist, in review. (227) Sabir J.S.M.*, Jansen R.K.*, Arasappan D., Calderon V., Noutahi E., Zheng C., Park S., Sabir M.J., Baeshen M.N., Hajrah N.H., Khiyami M.A., Baeshen N.A., Obaid A.Y., Al-Malki A.L., Sankoff D., El-Mabrouk N. and Ruhlman T.A. 2016. The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae. Scientific Reports, in review. *co-first authors. (228) Ashworth M.P., Lobban C.S., Witkowski A., Theriot E.C., Sabir J.S.M., Sabir M.J., Alharbi N.S. and Jansen R.K. 2016. Molecular and morphological investigations of stauros-bearing, raphid pennate diatoms (Bacillariophyceae): Craspedostauros E.J. Cox and Staurotropis T.B.B. Paddock and their relationship to the rest of the Mastogloiales. Protist, in review. (229) Gruenstaeudl M., Carstens B.C., Santos-Guerra A., and Jansen R.K. 2016. The impact of hybrid taxa on ancestral area reconstructions of Tolpis (Asteraceae). Biological Journal of the Linnaean Society, in review. (230) Schwarz E.N., Ruhlman T.A., Weng M.-L., Khiyami M.A., Sabir J.M.S., Hajarah N.H., Alharbi N.S., Rabah S.O., and Jansen R.K. 2016. Plastome-wide nucleotide substitution rates reveal accelerated rates in Papilionoideae and correlations with genome features across legume subfamilies. Journal of Molecular Evolution, in review. (231) Hansen D.R., Jansen R.K., Sage R.F, Villasenor J.L. and Simpson B.B. 2016. Molecular phylogeny of Pectis (Tageteae, Asteraceae), A C4 genus of the neotropics, and its sister genus Porophyllum. Lundellia, in review. (232) Weng M.-L., Ruhlman T.A. and Jansen R.K. 2016. Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes. New Phytologist, in review.

Papers Presented at National and International Meetings (since 2006 only):

Guisinger-Bellian, Mary, Chumley, Timothy, Kuehl, Jennifer, Boore, Jeffrey, Jansen, Robert K. Organization and Evolution of Chloroplast Genomes in the Flowering Plant Family Geraniaceae. Annual Meeting of the Society for Molecular Biology and Evolution, May 24-28, 2006, Arizona State University, poster presentation. Hansen, Debra, Zhengqiu, Cai, Boore, Jeffrey L., Kuehl, Jennifer V., Jansen, Robert K. Complete chloroplast genome sequences of Illicium (Schisandraceae) and Buxus (Buxaceae): Genome organization and implications for phylogeny of angiosperms. Annual Meeting of the Botanical Society of America, July 28-August 2, 2006, Chico, CA, poster presentation. Zhengqiu, Cai, Peñaflor, Cynthia, Leebens-Mack, Jim, Kuehl, Jennifer V., Carlson, John, dePamphilis, Claude W., Boore, Jeffrey, Jansen, Robert K. Complete chloroplast genome sequences of Drimys, Liriodendron, and Piper: Implications for the

28 phylogeny of magnoliids and evolution of GC content. Annual Meeting of the Botanical Society of America, July 28-August 2, 2006, Chico, CA, poster presentation. Steele, Roxi, Gilbert, Larry, Jansen, Robert K. Identifying Informative Chloroplast Markers for Examining Phylogenetic Relationships Within Psiguria (Cucurbitaceae). Annual Meeting of the Botanical Society of America, July 28- August 2, 2006, Chico, CA, poster presentation. Dastidar, Sayantani, Zhengqiu, Cai, Peñaflor, Cynthia, Kuehl, Jennifer V., Boore, Jeffrey L., Jansen, Robert K. Identifying Informative Chloroplast Markers for Examining Phylogenetic Relationships Within Psiguria (Cucurbitaceae). Annual Meeting of the Botanical Society of America, July 28-August 2, 2006, Chico, CA, poster presentation. Jansen, Robert K., Zhengqiu, Cai, Hansen, Debra, Dastidar, Sayantani, Peñaflor, Cynthia, Timme, Ruth, Hansen, Katie, Haberle, Rosemarie C., Chumley, Timothy W., Guisinger-Bellian, Mary M., Daniell, Henry, Lee, Seung-Bum, Raubeson, Linda A., Peery, Rhiannon, dePamphilis, Claude W., Leebens-Mack, Jim, McNeal, Joel R., Boore, Jeffrey, Kuehl, Jennifer V. Phylogeny of angiosperms based on whole chloroplast genome sequences. Annual Meeting of the Botanical Society of America, July 28-August 2, 2006, Chico, CA, oral presentation. Raubeson, Linda A., McCoy, Skip K R, Müller, Kai, Wall, P. Kerr, Leebens-Mack, Jim, Boore, Jeffrey L., Jansen, Robert K., dePamphilis, Claude W. Seed plant phylogeny based on sequences from 61 (mostly) shared plastid genes. Annual Meeting of the Botanical Society of America, July 28-August 2, 2006, Chico, CA, oral presentation. Hansen, Katie; Blazier, Chris; Rehman, Sumaiyah, Kuehl, Jennifer V., Boore, Jeffrey L., Jansen, Robert K. Comparative Chloroplast Genomics in Passiflora. Botany and Plant Biology 2007 Joint Congress, July 7-11, 2007, Chicago, Illinois. Ruck, Elizabeth, Andersen, Robert, Theriot, Edward, Jansen, Robert K., Cattalico, Rose Ann, Rocap, Gabrielle, Julius, Mathew, Draisma, Stefano, Kawai, Hiroshi, Ashworth, Matt P., Zhengqiu, Cai, Ong, Han. Current Progress Towards an Algal Heterokont Tree of Life. Botany and Plant Biology 2007 Joint Congress, July 7-11, 2007, Chicago, Illinois. Zhengqiu, Cai, Kim, Hyi-Gyung, Ruck, Elizabeth, Guisinger-Bellian, Mary M., McMurtry, Vanity, Boore, Jeffrey L., Jansen, Robert K. Extensive rearrangements in the plastid genome of Trifolium subterraneum (Fabaceae) are associated with numerous repeated sequences and novel DNA insertions. Botany and Plant Biology 2007 Joint Congress, July 7-11, 2007, Chicago, Illinois. Steele, Roxi, Guisinger-Bellian, Mary M., Jansen, Robert K., Linder, Randal. Identifying Useful Low-copy Nuclear Markers for Examining Phylogenetic Relationships within Angiosperms. Botany and Plant Biology 2007 Joint Congress, July 7-11, 2007, Chicago, Illinois. Goodson, Barbara, Rehman, Sumaiyah, Santos-Guerra, Arnoldo, Jansen, Robert K. Molecular systematics and biogeography of Descurainia Webb & Berthel. (Brassicaceae) based on nuclear ITS and non-coding chloroplast DNA. Botany and Plant Biology 2007 Joint Congress, July 7-11, 2007, Chicago, Illinois. Guisinger, Mary M, Kuehl, Jennifer V., Boore, Jeffrey L., Jansen, Robert K. Genome- wide analyses reveal patterns of increased nonsynonymous substitutions in the flowering plant family Geraniaceae. Botany 2008, July 26-30, Vancouver, BC. Ruck, Elizabeth, Ashworth, Matt P., Nakov, Teofil, Zhengqiu, Cai, Theriot, Edward, Jansen, Robert K., Andersen, Robert, Julius, Mathew, Draisma, Stefano, Kawai,

29 Hiroshi. Assessing multi-gene candidates for an algal heterokont phylogeny. Botany 2008, July 26-30, Vancouver, BC. Hansen, Debra R., Jansen, Robert K., Simpson, Beryl. Phylogeny and biogeography of Pectis and Porophyllum (Asteraceae, Tageteae). Botany 2008, July 26-30, Vancouver, BC. Steele, Roxi, Gilbert, Larry, Jansen, Robert K. Systematics of the Neotropical Genus Psiguria (Cucurbitaceae). Botany 2008, July 26-30, Vancouver, BC. Haberle, Rosemarie, Dang, Ashley, Lee, Tammy, Peñaflor, Cynthia, Cortes-Burns, Helen, Oestreich, Andrea, Raubeson, Linda A., Cellinese, Nico, Kim, Sang-Tae, Edwards, Erika, Eddie, William M.M., Jansen, Robert K. Taxonomic and biogeographic implications of a three-gene phylogeny of the Campanulaceae sensu stricto. Botany 2008, July 26-30, Vancouver, BC. Wojciechowski, Martin F., Daniell, Henry, Jansen, Robert K. Phylogenetic distribution of intron losses from the plastid clpP and rps12 genes among legumes (Leguminosae). Botany 2008, July 26-30, Vancouver, BC. Gruenstaeudl, Michael, Park, Seon-Joo, Santos-Guerra, Arnoldo, Jansen, Robert K. Phylogenetic relationships in Tolpis (Asteraceae) and the utility of ETS sequence variation despite incomplete rDNA homogenization. Botany 2008, July 26-30, Vancouver, BC. Jansen, Robert K., Ruck, Elizabeth, Ashworth, Matt P., Nakov, Teofil, Zhengqiu, Cai, Theriot, Edward, Andersen, Robert, Julius, Mathew, Draisma, Stefano, Kawai, Hiroshi. Assessing multi-gene candidates for an algal heterokont phylogeny. Protist2008, July 21-26, Halifax, NS. Theriot, Edward C., Ashworth, Matthew, Jansen, Robert K., Nakov, Teofil, Ruck, Elizabeth, Zhengqui, Cai. A multigene approach to inferring the diatom phylogeny: congruence and conflict. Phycological Society of America 2008 annual meeting. July 27-30, New Orleans, LA. Ashworth, Matt P., Ruck, Elizabeth, Nakov, Teofil, Zhengqiu, Cai, Theriot, Edward, Jansen, Robert K., Andersen, Robert, Julius, Mathew, Draisma, Stefano, Kawai, Hiroshi.Assessing multi-gene candidates for an algal heterokont phylogeny. Phycological Society of America 2008 annual meeting. July 27-30, New Orleans, LA. Blazier, Chris, Guisinger, Mary M, Jansen, Robert K. Gene loss and reductive rearrangement of the plastid genome throughout a divergent angiosperm clade. SMBE 2009, June 3-7, 2009, Iowa City, IA. Gruenstaeudl, Michael, Santos-Guerra, Arnoldo, and Jansen, Robert K. Time and sequence of dispersal events in the Macaronesian island lineage Tolpis - testing the utility of event- and model-based inference. Botany 2009, Snowbird, Utah, July 25- 29. Guisinger, Mary M., Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, and Robert K. Jansen. Rates and patterns of plastid genome evolution in the grasses. ASPB 2009, Honolulu, HI, July 18-22, 2009. Theriot, Edward C., Ruck, Elizabeth, Ashworth, Mathew, Nakov, Teofil, Jansen, Robert K. A preliminary multigene phylogeny of the diatoms. ASPB 2009, Honolulu, HI, July 18-22, 2009. Blazier, C., Ruhlman T, Jansen, R.K. Phylogenetic distribution of gene loss from plastid and mitochondrial genomes in Erodium (Geraniaceae). 2nd International Symposium on Chloroplast Genomics and Genetic Engineering. June 20-23, 2010, Maynooth, Ireland.

30 Ruhlman T, Jansen, R.K. Casualities of plastid genome evolution in Geraniaceae. How do plastids deal with high sequence divergence in an essential RNA polymerase gene? 2nd International Symposium on Chloroplast Genomics and Genetic Engineering. June 20-23, 2010, Maynooth, Ireland. Weng, M.-L., Gibby, M., Jansen, R.K. A phylogenetic analysis of Pelargonium based on three plastid genes. Poster presented at the 2010 Botanical Society of America meetings in Providence, RI. Hansen, D.R., Jansen, R.K., Sage, R.F., Simpson, B. Phylogenies of Pectis and Porophyllum (Asteraceae, Tageteae) inferred from ITS and chloroplast sequence data. Oral presentation at at the 2010 Botanical Society of America meetings in Providence, RI. Quedensley, T.S., Jansen, R.K. Phylogeny of the Roldana-clade (Asteraceae: Senecioneae): Montane forest endemism and diversity. Oral presentation at the 2010 Botanical Society of America meetings in Providence, RI. Weng, M-L, M. Gibby, and R.K. Jansen. 2011. Heterogeneity of nucleotide substitution rates in organelle genes of Pelargonium (Geraniaceae). 2011 SMBE meeting, Kyoto Japan, July 26-30. Jansen, R.K., Gruenstaeudl, M., Hawkes, C., Santos-Guerra, A. Phylogenetic relationships of Tolpis and Diversification between Plants and their Associated Arbuscular Mycorrhizal Fungi in Macaronesia. Botanical Society of America meetings in Columbus, Ohio, July 11, 2012. Jin Zhang, Tracey A Ruhlman, Robert K Jansen, Evolution of sigma factors in Geraniaceae, 3rd International Symposium on Chloroplast Genomics and Genetic Engineering, May 8 - 11, 2013, New Jersey. Weng, M.-L., J. C. Blazier, and R.K. Jansen. 2013. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats and nucleotide substitution rates. Society for Molecular Biology and Evolution 2013 Annual Meeting, Chicago, USA. Jin Zhang, Tracey A Ruhlman, Robert K Jansen, Evolution of sigma factors in Geraniaceae, Annual Meeting of the Society for Molecular Biology and Evolution, July 7 - 11, 2013, Chicago Weng, M.-L., T. R. Ruhlman, and R.K. Jansen. 2014. Plastid-nuclear interaction and accelerated coevolution in plastid ribosomes. Society for Molecular Biology and Evolution 2014 Annual Meeting, San Juan, Puerto Rico. Weng, M.-L., T. R. Ruhlman, and R.K. Jansen. 2015. Plastid-nuclear interaction and accelerated coevolution in plastid ribosomes. Gordon Conference on “Chloroplast Biotechnology” in Ventura CA.

Grant Support:

Past Support

NSF (Biological Research Resources Program), high density mobile cabinet storage in the Beal-Darlington Herbarium, 1983-1985, substitute P.I. from Dec 1983 - Jun, 1984. ($130,760). NSF (Systematic Biology Program), Molecular Systematics of the Asteraceae, Dec 1984 - Dec 1986. Co-P.I. with Dr. Jeffrey Palmer. ($165,000). University of Connecticut Research Foundation, "Chloroplast DNA Systematics of the Lettuce Tribe (Cichorieae-Asteraceae) ," Jan 1987 - Jan 1988 ($20,521).

31 NSF (Systematic Biology Program), "Molecular Systematics of the Tribe Cichorieae," Oct 1987 – Oct 1990 ($200,971). NSF (Visiting Professorship for Women), "Chloroplast DNA as a tool in the systematics of Vernonia (Vernonieae: Asteraceae) ," Aug 1988 - Jul 1989 ($95,878) - sponsoring scientist for Dr. Sterling C. Keeley. University of Connecticut Research Foundation, "Rotor for Ultracentrifuge," ($7,000). NSF (Systematic Biology Program), "Systematic studies of Solanum section Basarthrum," Jun 1989-Jun 1991 ($107,458) - co-P.I. with Dr. Gregory Anderson. University of Connecticut Research Foundation, "Evolution of the sunflower tribe (Heliantheae: Asteraceae) based on gene sequencing and restriction site variation of chloroplast DNA," Oct 1989 -Sept 1990 ($10,710). University of Connecticut Research Foundation, "Two Beckman rotors and accessories," Dec 1989-May 1990 ($23,817). NSF (Doctoral Dissertation Program), "Two Modes of Speciation in Coreopsis (Asteraceae): A Chloroplast DNA Study," 15 Apr 1990 - 15 Apr 1990 -15 Apr 1992 ($9,990) - Co-PI with Kent Holsinger and Roberta Mason. Alfred P. Sloan Foundation, "Phylogeny of the subfamily Asteroideae based on rbcL gene sequences and chloroplast DNA restriction site variation," Feb 1990-Feb 1991 ($40,250) - sponsoring scientist for Dr. Ki-Joong Kim. NSF (Minority Research Initiation), "Phylogenetic Studies of DNA and Morphological Variation in the subtribe Ecliptinae," Jun 1991 - Dec 1993 ($230,500) - sponsoring scientist for Dr. Jose Panero. NSF (Systematic Biology Program), "Phylogenetic and Molecular Evolutionary Studies of Chloroplast DNA Variation in the Asteraceae," Mar 1991- Feb. 1994 ($243,614). NSF (Doctoral Dissertation Program), "Systematics and Biogeography of Mentzelia (Loasaceae): a North and South American Desert Disjunct,” Mar 1993 - Mar 1995 ($10,000) - co-PI with Ms. Alice Hempel. NSF (Doctoral Dissertation Program), "Phylogenetic and Molecular Evolutionary Studies of the Tageteae (Asteraceae),” Jul 1994 - Jun 1996 ($10,000) - co-PI with Mr. Dennis J. Loockerman. American Orchid Society "Systematics of the Genus Calopogon and the Tribe Arethuseae,” Dec 1996 - Jul 1997 ($4,550) - co-PI with Mr. Douglas H. Goldman. NSF (Systematic Biology Program), "Phylogeny and Character Evolution of Basal Asteraceae Lineages,” Mar 1994 - Feb 1998 ($195,000). NSF (Doctoral Dissertation Improvement) "Phylogenetic Implications of Hybridization in the Phlox pilosa Complex (Polemoniaceae): Diploid Hybrid Origin of Taxa?" May 1996 - Apr 1998 ($10,000) - co-PI with Ms. Carolyn Ferguson. NSF (Doctoral Dissertation Improvement) "Systematics of Calopogon and the Arethuseae (Orchidaceae),” May 1996 - Apr 1998 ($10,000) - co-PI with Mr. Douglas H. Goldman. NSF (Doctoral Dissertation Improvement) " Systematics of Spigelia (Loganiaceae): Tropical/Temperate Relationships and the Origin of a Temperate Disjunction,” May 1996 - Apr 1998 ($9,930), co-PI with Dr. Billie L. Turner and Ms. Katherine R. Gould. NSF (Doctoral Dissertation Improvement) "Origin and Evolutionary Relationships of the Cultivated Passion Fruit,” Jun 1997 - May 1999 ($10,000) - co-PI with Dr. Lawrence Gilbert and Ms. Anne K. Hansen. NSF (Doctoral Dissertation Improvement) "Origin and Evolution of Endemic Sideritis (Lamiaceae) from the Macaronesian Archipelagos,” Jun 1998 - May 2000 ($10,000)

32 - co-PI with Ms. Jan Barber. NSF (Systematic Biology Program), "Origin and Evolution of Endemic Asteraceae from the Macaronesian Archipelagos,” Sep 1997 - Dec 2000 ($164,987). National Geographic Society "Biogeography and Evolution of Endemic Asteraceae of Macaronesian Archipelagos,” Feb 1998 - Dec 2000 ($18,600) - co-PI with Dr. Arnoldo Santos-Guerra. NSF (Doctoral Dissertation Improvement) “The Role of Hybridization in the Evolution of Argyranthemum in Macaronesia,” Jun 1999 – May 2001 ($10,000) – co PI with Mr. Leslie Goertzen. US-Spain Science & Technology Program 2000 “Origin and evolution of the flora of the Canary Islands: A molecular phylogenetic approach to historical biogeography,” I Jun 2000 – 31 May 2001 ($17,800). NSF (Systematic Biology Program) “Phylogenetic and Molecular Evolutionary Investigations of Chloroplast DNA Variation in the Campanulaceae sensu stricto,” Mar 2000 – Feb 2003 ($200,105) – PI. NSF (Doctoral Dissertation Improvement) " The Roles of Edaphic Shifts and Long- Distance Dispersal in the Evolution of the American Desert Genus Tiquilia (Boraginaceae)," Jun 1 2002 - May 30 2004 ($10,000) - Co PI with Mike Moore. NSF (Doctoral Dissertation Improvement) " The Systematics and Biogeography of Menodora (Oleaceae)," Jun 1 2002 - May 30 2004 ($10,000) - Co PI with Tim Chumley. NSF (ITR/AP DEB) “Collaborative Research, “Computing Optimal Phylogenetic Trees under Genome Rearrangement Metrics,” Sep 1 2001 – 31 Aug 2005 ($288,030, includes 1 year no cost extension). NSF (IGERT) “Computational Phylogenetics and Applications to Biology,” Sep 1 2001 – Aug 30, 2007 ($2,699,106 includes 1 year no cost extension) – co PI with D. Hillis. R. Linder, R. Gutell, and T. Warnow. NSF (PEET) “Training New Diatom Systematists for New Priorities", Sep 1 2001 – Aug 30, 2007 ($737,543 included 1 year no cost extension) - co-PI with E. Theriot. NSF (ATOL) “Comparative Chloroplast Genomics: Integrating Computational Methods, Molecular Evolution, and Phylogeny,” Oct 1 2001 – Sep 30 2007 ($1,350,000 included 1 year no cost extension) – PI with two co-PIs (L. Raubeson and T. Warnow). NSF (Doctoral Dissertation Improvement Grant) "Dissertation Research: Systematics and Biogeography of the Neotropical Genus Psiguria (Cucurbitaceae)", Jun 1 2008 - May 31 2010 ($12,000) - co-PI with Pamela Steele. NSF (Sytematic Biology) " Phylogeny and Chloroplast Genome Evolution in Geraniaceae," 1 Sep 2007 - 28 Feb 2011 ($350,000). The Fred C. Gloeckner Foundation, Inc. “Plastid Transformation for Genetic Improvement of Pelargonium,” Sep 1, 2010 – Aug 30 2011 ($8,000) – co PI with Tracey Ruhlman. NSF (ATOL) "A phylogenetic and genomic investigation of the algal heterokont tree," Sep 15 2006 - Sep 14 2011 ($2,981,052 total, with $989,917 to UT-Austin) - co-PI with Ed Theirot. NSF (Plant Genome Program) “The Geraniaceae genomes project: Accelerated and coordinated evolution across the three plant genomes,” Jan 1 2011 – Dec 31 2015 ($2,420,822 total) – PI with three co-PIs (Tracey Ruhlman at UT-Austin, Jeff Palmer at Indiana and Jeff Mower at Nebraska).

33 Current Support

King Abdulaziz University, Saudi Arabia “Legume Plastid Genomics: Resources for Examining Genome Evolution and Genetic Engineering, Sep 1 2012 – Aug 31 2017 ($347,460), PI. King Abdulaziz University “Natural Products Genomics of Rhazya stricta: Phase I - Sequencing the Mitochondrial, Nuclear, and Plastid Genomes” Sep 1 2012 – Aug 31 2017 ($345,940), PI. King Abdulaziz University Saudi Arabia “Bioprospecting for High Lipid Content Producing Algae and Their Improvement by Plastid Transformation” Sep 1 2012 – Aug 31 2017 ($215,180), PI. NSF (Doctoral Dissertation Improvement) DISSERTATION RESEARCH: Phylogenomics and biogeography of Vochysia, unraveling its tempo and mode of evolution”, June 1, 2016 – May 30, 2018 ($20,069), PI with two co-PIs (Deise Pereira Goncalves and Beryl B. Simpson).

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