Professor, School of Integrative Plant Science Plant Biology Section
Theory and methodology of phylogenetic analysis
Systematics and taxonomy of the oak family
My research activities are rather broad, and be categorized as follows:
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 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, 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.
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 Anna Stalter, with some also by me, and volunteer Vern Durkee). 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 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 (as an example, 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 Peter Fraisenet, 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. 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. We now have have all Tompkins County specimens online.
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.
- Reveal, J. L., & Nixon, K. C. (2013). The palm type collection in the Liberty Hyde Bailey Hortorium (BH). Phytoneuron. 2013-79:#N/A.
- 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: A Journal for Botanical Nomenclature. 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.
- Salazar, J., & Nixon, K. C. (2008). New discoveries in the Canellaceae in the Antilles. Botanical Review. 74:103-111.
- Nixon, K. C. (2008). Paleobotany, evidence and molecular dating: An example from the Nymphaeales. Annals of the Missouri Botanical Garden. 95:103-111.
- Nixon, K. C. (2006). Global and neotropical distribution and diversity of oak (genus Quercus) and oak forests. Ecological Studies. 3-13.
- 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 Sciences. 167:737-749.
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 algorithms, 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 national 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 intensive 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.
406B Mann Library Building
Ithaca, NY 14853
kcn2 [at] cornell.edu