The Vision lab studies genome evolution and the architecture of complex traits, with a (non-exclusive) focus on the flowering plants. Among the questions we ask are:

• What is the genetic basis for ecologically important differences between species, and what evolutionary forces generate that variation?
• What mutational and evolutionary processes are responsible for the structural rearrangement of chromosomes among taxa?
• What effect do genome structural changes have on organismal phenotypes?

To address these questions, we use the tools of both molecular and computational biology, and are actively involved in the development of new computational methods.

Selected publications

Google Scholar Profile

CV

My research activities are diverse and span aspects of vegetation science from plant interactions to global patterns. However, the four projects described below serve to illustrate my current primary research interests. Please note that I am retired to the rank of Research Professor and no longer accept graduate and postdoctoral students, but I am continuing my research projects, continue to collaborate with colleagues, and continue to advise undergraduate research projects.

Community dynamics. Much of my early research at UNC focused on plant community dynamics, a topic that I have continued to investigate throughout my career. With students and collaborators I have made extensive use of permanent plots to address these kinds of questions. We recently completed an additional resurvey of forest demography plots (some dating back to 1934) and are using these data to address a broad range of questions including urban impact, evolving successional dynamics reflecting local and global change, and changes in productivity resulting from factors such as successional dynamics and changes in atmospheric CO₂.

Ecoinformatics. Ecoinformatics arrived as a subdiscipline of ecology only around the start of the 21^st century. I have been active during this period in developing the necessary cyber-infrastructure and addressing science questions in the area of ecoinformatics that draws on the increasing availability of data that document attributes of places, attributes of biological taxa (species), and records of occurrence and co-occurrence of species in specific places. In the past, studies of ecological communities were largely local case studies and no one knew how generalizable they were; many simply reflected the idiosyncrasies of a particular combination of time and space. We are now in a position to analyze community patterns over very large scales and assess their generality and the impacts of local contingencies.

Vegetation Classification. Formal, widely-adopted vegetation classifications are important for many purposes ranging from inventory to mapping to management prescription to simply documenting the context within which research has been conducted. In 1994 I established a collaboration consisting of the Ecological Society of American, the Nature Conservancy, the USGS and the US Federal Geographic Data Committee (with the US Forest Service as lead agency) to develop an open and scientifically credible US National Vegetation Classification (USNVC). We proposed national standards and in 2008 the Federal Geographic Data Committee adopted the key components as the US national standard. My research group and collaborators built the USNVC data archive in the form of VegBank.org, developed a peer-review system, and have completed the first formal revision and documentation of a significant set of Associations for the National Vegetation Classification.

Vegetation of the Carolinas. I have always been fascinated by the patterns of vegetation and biodiversity across landscapes. The Carolinas are remarkably diverse and the factors responsible for the vegetation of the region are poorly understood. In 1988, I established a collaboration to systematically document the natural vegetation of the Carolinas. Subsequently we have acquired and databased over 10,000 vegetation plots covering most of the over 500 USNVC vegetation types of the Carolinas. The resulting data are summarized on our website (cvs.bio.unc.edu) for use by applied scientists and the general public. In addition, we provide digital tools for predicting the natural vegetation of sites to guide restoration efforts.

Professional Service. I have and continue to contribute to the scientific community in numerous ways. I have served the International Association for Vegetation Science as President (2007-2011) and Publications Officer (2011-2015), I co-founded the Journal of Vegetation Science and served as one of the original Coeditors-in-Chief (1990-1995), I organized of the North American Section, and am active in efforts to establish international standards for vegetation data. I have served the Ecological Society of America as Secretary (1992-1995), Editor-in-Chief of Ecology and Ecological Monographs (1995-2000), and co-organizer of the Vegetation Section and the Southeastern Chapter, in addition to participating in numerous other roles.

Links to websites maintained by Prof. Peet and his collaborators:

• Carolina Vegetation Survey
• VegBank
• Duke Forest LTREB Project

My research group investigates the community ecology of infectious disease. We study pathogens infecting wild plants, chiefly grasses. Our main current interest is interactions between fungal pathogens and the broader leaf microbiome.

Adaptations are central to the study of evolution. Thus it is surprising that we know so little about the molecular basis of adaptive evolution. The goal of my research is to identify, clone, and characterize the evolution of genes underlying natural adaptations in order to determine the types of genes involved, how many and what types of genetic changes occurred, and the evolutionary history of these changes. These data will address key questions. For example, do adaptations involve many genetic changes or only a few? How important are regulatory versu! s amino acid changes in adaptation? How often are “new” gene s involved in adaptations? Are most adaptive alleles new mutations or pre-existing alleles segregating at low to moderate frequency within a species? Clearly, a deeper understanding of how genes change during adaptation will give insight into the potential and limits of adaptive evolution.

Spatial patterns of genomic features

I am also using genomic data to address important evolutionary questions. Recently, I used D. melanogaster genome sequence data to estimate genome-wide levels of gene clustering and to contrast the amount of clustering among genes with similar motifs to the levels of clustering in general. All chromosomes, except the fourth, showed substantial levels of gene clusteri! ng. Although not more clustered than the average pair of adjacent genes, genes with the same primary motif occur adjacent to one another more often than expected by chance. These results may mean that these small local groups of genes share regulatory elements and evolutionary histories.

Detecting natural selection in DNA sequence data

Molecular evolutionists have long sought to determine which changes within the protein coding and regulatory regions of a gene were shap! ed by natural selection. If an adaptive substitution has occurred in the recent past, there should be a paucity of DNA polymorphism surrounding the site under selection. Taking advantage of this fact, Andrew Kern and I have developed a permutation approach for detecting selected sites using polarized DNA polymorphism and divergence data. This method is especially useful for detecting the effects of weak selected forces across several loci. We used this approach to analyze a large DNA polymorphism and divergence data set of D. simulans genes. Surprisingly, although replacement fixations do not on average appear to be driven by selection, preferred codons – those codons that use the most abundant tRNA – have on average been fixed by selection. We plan to apply this method to additional data sets and to look at spatial patterns of nucleotide fixation within and around genes. For instance, one could see if there is a bias in the types of polymorphism (sy! nonymous vs. non-synonymous) nearest to a type of fixation. This would give insight into the dynamics of the fixation process and its impacts on adjoining variation.

Interaction of plants and microbes. I no longer supervise students or postdoctoral fellows. I remain a member of Jeff Dangl’s research group. The Dangl group investigates the plant immune system and its influence on the communities of environmental microbes associated with plants.

See publications here.

Broadly, I study the mechanisms of social behavior with an eye toward evolution. Like all neuroethologists, I am interested in understanding the mechanisms of behavior, in part, because understanding these mechanisms can inform our perspective on behavioral evolution by revealing the sensory, cognitive, or motor substrate on which selection acts to shape the behavior of organisms.

We study the social behavior of frogs because it is simple and easy to manipulate in both the lab and field. Ongoing projects include:

• the neural and hormonal mechanisms of mate choice in túngara frogs and spadefoot toads

• the neural and hormonal mechanisms of parental care in dart frogs, and

• the spatial cognition of dart frogs

Technically, our research employs molecular cloning, in situ hybridization, quantitative PCR, immunocytochemistry, radioimmunoassay, and behavior analysis.

I have taken an experimental approach to the study of evolution because it allows me to address questions from many areas of evolutionary biology. Evolution experiments using microorganisms have been able to address widely ranging topics from kin selection and the evolution of virulence to the evolution of mutation rates, and the evolution of habitat (or host) specialization.

Although I am interested in all aspects of evolutionary biology, and students and postdocs in my lab are encouraged to develop independent projects that follow their own interests, the primary focus of my work has been to investigate the genetics of adaptation. I am using laboratory evolution experiments of bacteriophage (bacterial viruses) to address the following questions:

• Does adaptation occur by large or small steps?
• Are certain genotypes better able to adapt than others?
• Can we identify factors that shape the nature of interactions between mutations?

Bacteriophage serve as particularly suitable systems for addressing the genetics of adaptation because they offer the opportunity to observe events on an evolutionary timescale within weeks or even days. For example, we can watch evolution of the bacteriophage phi-6 in action simply by monitoring increases in plaque size . As beneficial mutations appear and become common in adapting populations, fitness improves and plaque size increases.