Overview

I have diverse research interests in the theory and practice of plant systematics. My taxonomic interests include higher level analysis of seed plant and angiosperm relationships, and relationships of Hamamamelid and Rosid ordinal and family relationships. I work at the generic and species level within Fagaceae, and in particular in Quercus. I anticipate completion of the taxonomic treatment for Quercus for Flora Mesoamaricana this summer (2003). I am also very much involved in paleobotanical studies of Tertiary Fagaceae and a wide assortment of Late Cretaceous angiosperm floral remains in collaboration with Dr. W.L. Crepet. We are attempting to place a diverse Cretaceous flora into phylogenetic context and anticipate a rather extensive body of research in this area over the next few years. I also recently have developed a collaboration with Dr. David Dilcher (University of Florida) on early Cretaceous angiosperms of China, resulting in a publication in Science in 2002 describing what appears to be one of the first flowering plants. My theoretical interests center on methods of phylogenetic analysis, computer programs for analysis and display of phylogenetic trees, molecular and morphological information, supertree construction, molecular sequence alignment. I am also working on theory of diagnostic analysis, molecular diagnostics, and development of interactive morphological keys. My recent work has focused on developing algorithms for rapid parsimony analysis (although these can also be applied to maximum likelihood). I am currently working on new methods for faster DNA sequence alignment that should solve some existing problems that are limited by computation time. I have written several software packages, including CLADOS, DADA, Winclada, and Encino, that are used to analyze character distributions and augment other phylogenetic software such as NONA and Hennig86. I am coauthor of a new software package, TNT, with Pablo Goloboff and James S. Farris, that provides tools for rapid phylogenetic analysis of very large data matrices. In the area of biodiversity, I have developed a simple method for measuring phylogenetic diversity and thus maximizing sample diversity based on phylogenetic information. This method will be expanded and directly implemented in upcoming software that will provide priority lists for sampling while undertaking biological prospecting. I am also actively involved in both theoretical and practical approaches to bioprospecting. Finally, I have developed an extensive website system (www.plantsystematics.org, www.diversityoflife.org) that serves images of plants and animals, provides diagnostic interactive keys, and links all of these with specimen data, phylogenetic trees and classifications. The diagnostic programs I have developed run on desktops, handhelds, and through the web interface and are based on new algorithms for maximizing information retrieval.

Research Focus

I was originally hired without a laboratory (my duties were split among curation, research and extension). The lack of a laboratory for the first 20 years of my Cornell career limited my ability to undertake certain kinds of research (e.g., molecular systematics) and to obtain large grants, and shaped much of the direction that I have undertaken in my research. Given the lack of a wet laboratory, I was restricted to fieldwork, morphological, theoretical and methodological studies. In many ways this "limitation" allowed development of a research program focused on a range of issues that only required fieldwork, specimens, microscopes, and inexpensive computers. Possibly as a consequence of this, my research activities are rather broad, and can be categorized as follows: 1. Theory and methodology of phylogenetic analysis. 2. Phylogenetic relationships of higher seed plants and angiosperm groups. 3. Fossil history of angiosperms. 4. Systematics and taxonomy of Quercus (the oaks). and Fagaceae (the oak family). 5. Systematics of Platanaceae (the Sycamores). 6. Theory and methods of interactive diagnosis (simply put, interactive keying software and algorithms). 7. Software development for distributed parallel phylogenetic analysis. 8. Database structure and implementation for biodiversity and classification data. Over the past 4 years as curator of the herbarium, I have been intensely involved in the planning and move (both off and back onto campus) of the 850,000 specimen BH herbarium and associated facility. This involved a complete curation and reorganization of the collections (funded by a grant from the NSF) and consumed a fair amount of my attention. Now that the herbarium move and reorganization is essentially complete and for the first time I have my own laboratory, I plan to develop a two-pronged program and expand my morphological/anatomical studies of angiosperm diversity while also setting up a DNA isolation capability in my laboratory (especially since sequencing can now be easily and cheaply outsourced). I am close to completing a treatment for all Quercus for the New World (a culmination of research that I have undertaken over the past 30 years in the US/Canada, Mexico and Central America) and hope to use this background to resolve specific phylogenetic and biogeographic questions within Quercus using molecular markers (various approaches such as microsatellites are now showing some promise in Quercus). I also plan to continue my theoretical efforts in phylogenetic analysis, in particular to revisit the "parsimony ratchet" algorithm. This is one of my most important contributions (at least based on the number of citations the 1999 paper has received), and not only is widely used in parsimony software (e.g., TNT, Goloboff, Farris, Nixon 2001, 2003), but also has been adapted to maximum likelihood (e.g., Vos, 2003). In the only comparative study of likelihood tree search (Morrison, 2007), the "Nixon" ratchet was found to be one of the two most effective approaches to maximum likelihood tree search. Since publication of the algorithm, I have experimented with various modifications, some of which promise to further improve efficiency. I have not had adequate computer resources to fully test these modifications, but with the new Hortorium computer lab I now will have access to a sufficient number of computer cycles to fully explore the new algorithms (in off hours, of course). Over the past few years I have also been developing a new, very fast sequence alignment algorithm that utilizes block-generated information content to align multiple sequences heuristically. Although the theoretical issues have been resolved, I have not yet completed a full software implementation. This will be one of the goals over the next year. I will continue developing tools for delivery of biodiversity content, as can be seen at http://www.plantsystematics.org. Currently, I believe we have a greater representation of images of plant families and genera than any other resource on the web. While this may not be considered "research" in the strict sense, having immediate access to images of morphological features is a powerful tool that enhances and improves the efficiency of my higher-level phylogenetic studies, as well as our palobotanical research (fossil identifications) and of course for teaching. An important aspect of my future work that has significant outreach implications will be involvement in the Cultivated Flora of the United States, in collaboration with several other universities and botanical gardens. Part of this will involve development of new databases of biodiversity information focused on cultivated plants, and software for delivery of this information to the public. My additional goals for the next few years include completion of a fossil flora of our New Jersey Cretaceous flower sites in collaboration with Crepet and Gandolfo, and various taxonomic projects including in addition to Quercus a revision of the South American species of Nothofagus. I will be on sabbatical leave from September 15, 2008 through March 14, 2009 in Patagonia, Argentina. During this time I will continue developing software and work on algorithms, complete my monograph of Nothofagus, and continue biodiversity studies of South American plants, and continue collaborative work on angiosperm fossils with Crepet and Gandolfo.. b. Research Accomplishments 1. Theory and methodology of phylogenetic analysis. My background in this area includes several papers focusing on various theoretical issues in phylogenetic analysis, and software implementations of "user-friendly" programs for data visualization and analysis. Perhaps my most important contribution in this area was development of a rapid tree-search algorithm (the "parsimony ratchet") that uses a directed random walk by iteratively reweighting variables to increase efficiency of tree search. The parsimony ratchet was the first of the 'rapid" methods that are now available for tree search, and improved tree search efficiency and effectiveness by orders of magnitude over existing strategies as implemented in PAUP. I first implemented the algorithm through the program NONA (written by Pablo Goloboff) and it has since been implemented in at least two versions that utilize PAUP* (e.g., Sikes and Lewis, 2001), as well as in TNT (Goloboff, Farris and Nixon, 2001, 2003). The ratchet has been successfully employed to analyze some of the largest data sets in plant systematics, e.g., the 500 taxon chloroplast data set (Nixon, 1999) and 567 taxon 3-gene data set (Soltis et al., 2000) and is now commonly used in calculation of supertrees. 2. Phylogenetic relationships and diversity of higher seed plants and angiosperm groups. This is intimately tied with the paleobotanical research in collaboration with Crepet and Gandolfo here at Cornell (and others outside of Cornell). I have been involved in several large analyses of seed plant/angiosperm relationships, beginning with a morphological analysis (Nixon et al., 1994) and the first combined molecular/morphological analysis (Albert et al., 1994) and continuing with reanalysis of the 500-taxon rbcL data set (Nixon, 1999; Davis, Nixon, and Little 2004), the original analysis of the "3-gene" angiosperm data set (Soltis et al., 2000) and the combined molecular/morphological analysis of Archaefructus (Sun et al. 2000). I plan to continue these large-scale analyses, combining new approaches for the analysis of large data sets (e.g., the parsimony ratchet and Goloboff tree search methods) with new morphological data sets over large numbers of taxa. 3. Fossil history of angiosperms. I have a long standing research program in fossil angiosperms, beginning with a review of Tertiary fossil oaks in my Ph.D. thesis, continuing with papers on the earliest fossil evidence of Fagaceae in the Tertiary, and continuing with studies of Cretaceous fossil flowers in collaboration with Crepet and Gandolfo (see publication list). My role in these collaborative studies has been to apply my knowledge of angiosperm diversity and identification (see teaching section) in preliminary fossil identifications, followed by intensive cladistic analysis of morphological or combined morphological/molecular datasets to accurately and reproducibly identify fossils. Our studies of Cretaceous fossil flowers remain the most extensive, and I believe the most completely analyzed, of any angiosperm fossil flower sites, and provide the best view of the Late Cretaceous diversification of angiosperms into modern taxonomic groups. These papers will remain important for an indefinite period of time as documentation of this diversity, and are useful in providing calibration points for molecular dating studies. I also was invited to collaborate on an analysis of what may be the oldest angiosperm fossil flower, Archaefructus. My role in this paper was to develop the morphological matrix for extant seed plants, combine this with a selected three-gene data set, and analyze with our tools for large data set analysis. 4. Systematics and taxonomy of Quercus (the oaks). and Fagaceae (the oak family). I am the de facto expert on North American Quercus (I authored the treatment of Fagaceae including the beeches and chestnuts) and Quercus for Flora North America, which includes the U.S. and Canada). I am currently in the final phases of completing the treatment of Quercus for Flora Mesoamericana, covering the region From Chiapas, Mexico to Panama (I am recognizing 40 species in this area). Recently, a species of oak from Guerrero, Mexico was named in my honor (Quercus nixoniana Valencia & ) although it is likely that I will eventually place it in synonymy under another species name. I also have a fungus named after me by a former student (). 5. Systematics of Platanaceae (the Sycamores). The sycamores are an extremely important genus that was poorly understood prior to publication of a comprehensive monograph of the North American species (Nixon & Poole, 2003). I began work (not part of my Ph.D. thesis) on this group while a graduate student in Texas, based on my extensive fieldwork in Mexico, and was able to complete this work fairly recently (Nixon & Poole, 2003). In the context of this study we named two new and undescribed species from Mexico. I consider this to be one of my most important taxonomic contributions, given the previous confusion and misunderstanding surrounding how many species of Platanus are present in Mexico, inadequate description of their morphology, and the importance of this group in the early fossil history of flowering plants. 6. Theory and methods of interactive diagnosis (simply put, interactive keying software and algorithms). I have developed (as yet unpublished) algorithms for expediting specimen identification through interactive keys that allow selection of most efficient paths based on the level of expertise and background knowledge of the user (keys can be weighted for either experts or students, for example). An example of such a key can be seen at my website http://www.plantsystematics.org. 7. Software development for distributed parallel phylogenetic analysis. In addition to developing software for PCs that aids in phylogenetic analysis (Winclada), and being a coauthor on the program TNT (Goloboff, Farris and Nixon, 2001) I am currently developing web-based interfaces that allow distributed analyses using multiple software packages across heterogeneous arrays of computers (Linux, Windows and MacIntosh) based on a simple Perl client/Adobe server/MySQL server model. An important aspect of this system is a relational database model for storage of analytical methods along with databased results, which alleviates many of the issues in managing large numbers of analyses across a single or many permutations of a data set. This system also allows users to contribute computation resources based on the usage of their machine, capabilities (e.g., speed and ram) and what software they have licensed to perform multiple, simultaneous analyses. The system has been implemented as part of my teaching plan, and I am currently also training two graduate students in programming database and web interfaces as part of development of the package. 8. Bioinformatics: Database structure and implementation for biodiversity and classification data. Ancillary to development of a large database and web delivery system for phylogenetic, taxonomic, and biodiversity data (see http://www.plantsystematics.org), I have developed database structures for storage of complex tree-like relationships inherent in taxonomic names. This system provides easy ways to contrast different classification systems and retrieve name usage across different classifications. Currently, the system is focused on delivery of images, interactive maps, and interactive keys for all families and genera of angiosperms, gymnosperms, and ferns (i.e., the vascular plants). I will continue to expand this project to include more types of data. Morrison, David A. 2007 Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences. Systematic Biology, 56:6, 988 - 1010. Sikes, D.S. and P.O. Lewis. 2001. PAUPRat: PAUP* implementation of the parsimony ratchet. Software. Version, 2001. Vos, R. A. 2003. Accelerated likelihood surface exploration: The likelihood ratchet. Syst. Biol. 52:368–373.

Outreach and Extension Focus

My direct extension activities involve overseeing plant identification services conducted at the herbarium. The constituents include a wide variety of users including extension agents, agriculturists, local gardeners, farmers, and various individuals with questions about plant identification. Typically, this includes horticultural plants, weeds, natives, and sometimes fruits and materials from foreign countries. My outreach activities include development of websites for plant identification, image serving and mapping of plants (www.plantsystematics.org). As part of this project, we also have developed the “Tompkins County Flora” which provides images, maps and other information about all of the plants that occur naturally in Tompkins County. My extension program is largely implemented through the L.H. Bailey Herbarium, of which I am curator. Our herbarium has two major strengths, native plants of Central New York, and cultivated plants. In addition to administering a plant identification service through the herbarium staff (most identifications are made by Associate Curator Ed Cope, with some also by me and by our former Assistant Curator Bob Dirig). Over the past few years we have not kept exact counts of the number of specimens identified as an extension service, but they are summarized below. Other aspects of our outreach, related directly to Extension, is the development of web tools for identification of plants by visual comparison with verified images. This is available at http://www.plantsystematics.org and constitutes one of the most complete and accessible plant identification websites, with ca. 2,000 distinct users per day, and more than 2 million downloads per year. Native Plant Identificatons: We make approximately 150 plant identifications a year for the public and Cornell community (in 2007, ca. 65 by Ed Cope, 96 by Bob Dirig, 15 by Kevin Nixon) and answer at least another 50-100 requests for miscellaneous plant-related information, including requests for information about cultivated plants using Ethel Zoe Bailey Nursery and Seed Catalogue Collection (these requests are mostly handled by Sherry Vance, under my supervision). In addition to accepting plant material and/or images directly for identification, we now have a project called the "Tompkins County Flora" which provides a web interface with searchable databases of both specimen and locality data as well as linked live and herbarium images of all vascular plants known to occur in the wild in Tompkins County. This website is accessible at: http://www.plantsystematics.org/tompkins.html. Recently we received a grant from the BRI program to completely digitize label data and database specimen images for all of our ca. 20,000 herbarium specimens from Tompkins County, and this is proceeding very well, the imaging being done by Anna Stalter under my supervision. By early 2009, we should have all specimens online, both in terms of label data and images, including closeups of diagnostic features. Cultivated Plant Program. The herbarium is one of the most important repositories of cultivated plant specimens in North America, and we are in the process of developing databased web interfaces that will extend the important works of L.H. Bailey (most importantly, Hortus Third) which is now outdated. We are developing an entirely new project, called Hortus Americanus, and in addition to species and cultivars covered in Hortus Third will have additional species included based on databases that we have constructed using our Nursery and Seed Catalogue Collection (the Ethel Zoe Bailey Collection). These databases, since they are still incomplete, are not yet available online, but will become part of the collaborative project being developed with the Missouri Botanical Garden (Peter Raven) and the National Arboretum (Thomas Elias). Currently, we have ca. 3500 cultivated genera databased, which is about 10% greater than the coverage of Hortus Third. The timeframe on completion of this project will depend partly on funding from outside sources. Selected Publications Citing our Herbarium (BH) From 2007 (we cannot provide a full list, since we often are not notified of citations). Dirig, R. 2007. A treasury of spring wildflowers and their butterflies: A prelude to what is stirring in New York from April to June, arranged by calendar and habitat. Clintonia, Magazine of the Niagara Frontier Botanical Society, Inc. 22 (issue 2): 9. *Hodel, D. R. 2007. Unravelling Clinostigma in Samoa. Palms, Journal of the International Palm Society 51(1): 11-29. Kass, L., & E. Cobb. 2007, fall. Landmarks and milestones in American plant biology: the Cornell connection. Plant Science Bulletin 53(3): 90-101. [Also available online, Sept. 2007: http://www.botany.org/plantsciencebulletin/psb-2007-53-3.pdf] Kass, L., R. Hunt, S. Danforth, & T. Egan. 2007, Feb. Reproductive biology of Buttonwood, a polygamous population on San Salvador. Bahamas Naturalist & Journal of Science 2(1): 40-49. Kass, L. B., R. E. Hunt, S. B. Danforth, & T. Egan. 2007. Reproductive biology of Buttonwood (Conocarpus erectus L.; Combretaceae), a polygamous population on San Salvador Island, Bahamas, pp. 31-42. In: Rathcke, B. J. & W. K. Hayes (eds.), Proceedings of the 11th Symposium on the Natural History of the Bahamas, 2005, Gerace Research Center, San Salvador Island, Bahamas. Kass, L. B. 2007. Illustrations for the Flora of the Bahama Archipelago revisited, pp. 26-30. In: Rathcke, B. J. & W. K. Hayes (eds.), Proceedings of the 11th Symposium on the Natural History of the Bahamas, 2005, Gerace Research Center, San Salvador Island, Bahamas. Kass, L. B. 2007. Barbara McClintock (1902-1992), on Women Pioneers in Plant Biology, American Society of Plant Biologists website, published online, March 2007: http://www.aspb.org/committees/women/pioneers.cfm#McClintock

Teaching Focus

TEACHING GOALS Although I was hired without a teaching component, and my job description still does not include one, I feel strongly that teaching is an important aspect of maintaining an active and vigorous research program. My focus in teaching has been on graduate courses in advanced Plant Systematics - a Tropical Plant Families course, and a course on theory and methods of analysis in Phylogenetic Systematics. I also lead a graduate discussion group every semester that focuses mostly on analytical methods. These courses are important to my research because they help to keep me abreast of new developments in plant systematics and evolutionary biology. Beginning in Fall, 2009, I now teach an undergraduate course entitled "Global Vegetation and Plant Biodiversity" (Biopl 2300) intended for students with a minimal botanicla background. This course emphasizes the factors controlling the distribution of vegetation and addresses issues of plant biodiversity from the context of climate and human disturbance. Associated with this course is an optional field course which spends 3 weeks in Patagonia studying vegetation. This course has been successful, with three field trips so far (2010, 2011, 2012) with a total of 47 undergraduates. Based on responses from students, many consider this trip to be the most significant aspect of their Cornell education. Perhaps the most important course I have taught over the years is Phylogenetic Systematics. This course has been focused on phylogenetic analysis using parsimony, with lesser components on other approaches such as phenetics, maximum likelihood, "Bayesian" analysis as used in phylogenetics, biogeography and coevolution. Because I have developed algorithms and software in these areas, the course has evolved considerably over the years. The lecture and laboratory exercises for this course were completely revised for the Spring 2009 semester. This is an outgrowth of an experimental approach to teaching this material that I have undertaken in my discussion group (team-taught with Jerry Davis). Under this model, the students are required to reanalyze published material using multiple methods, first attempting to duplicate the published results, then extending the analyses to include various alignment algoritms, parsimony, maximum likelihood, Bayesian analysis, and other methods appropriate to the particular studies. This teaching by example approach prepares our graduate students for the realities of publishing their own work, and gives them knowledge and tools that will improve their chances of succeeding when they present their own work at job seminars or natio0nal meetings. At the same time, by reanalyzing existing published analyses, they better understand pitfalls and in some cases, ideas for new research questions emerge for many of the students. The skills developed in this course will be extended and honed through our weekly discussion group for students who have completed the course. Another undergraduate/graduate course that I teach is "Tropical Plant Families" which includes a field trip to a Latin American country to study flowering plant diversity with an emphasis on field identification at the family level. The course is composed mostly of graduate students from Plant Biology, with a few undergraduates and graduate students from Entomology and/or Ecology and Evolutionary Biology. This course is an intensiive overview of angiosperm diversity that both prepares students for teaching field courses as well as provides experience with a multitude of plant families, potentially providing ideas for future research projects. It also prepares students for the kind of tropical field work they will need to undertake in most modern systematic studies. For the past 14 years, I have taught in the summer OTS (organization for Tropical Studies) course "Tropical Plant Systematics" in Costa Rica by invitation. This is a team-taught course with visiting faculty from around the US and Costa Rica. In this course I generally cover phylogenetics/cladistic analysis, theory of classification, and also teach field identification by leading hikes through tropical forest habitats. I usually am there for about two weeks of the eight week course.

Additional Links

• Tompkins County Flora
• Fossil Flowers
• Liberty Hyde Bailey Hortorium
• Link to CALS Research and Impact
• Link to Research & Expertise Across Cornell

Selected Publications

Journal Publications

• Nixon, K. C., & Carpenter, James, (2012). More On Homology. Cladistics. 28:225-226.
• Avalos, S., Nixon, K. C., & Kelly, L. (2011). Quercus delgadoana (Fagaceae), a New Species from the Sierra Madre Oriental, Mexico. Novon. 21:274-277.
• Gandolfo Nixon, M. A., Hermsen, E. J., Zamaloa, M. C., Nixon, K. C., Gonzalez, C. C., Wilf, P., Cuneo, N. R., & Johnson, K. R. (2010). Oldest Known Eucalyptus Fossils Are from South America. PLoS One. 6:e21084.
• Nixon, K. C., (2008). Paleobotany, evidence and molecular dating: An example from the Nymphaeales. Annals Missouri Botanical Garden. 95:103-111.
• Salazar, J., & Nixon, K. C. (2008). New discoveries in the Canellaceae in the Antilles. Botanical Review. 74:103-111.
• Rothwell, G. W., & Nixon, K. C. (2006). How does the inclusion of fossil data change our conclusions about the phylogenetic history of Euphyllophytes. International Journal of Plant Science. 167:737-749.
• Nixon, K. C., (2006). Global and neotropical distribution and diversity of oak (genus Quercus) and oak forests. Ecological Studies. 3-13.

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