Overview
My current research covers the population genetics, biogeography, and systematics of beetles. This work focuses on the plum curculio beetle, a fruit pest native to the eastern United States. This beetle is an obstacle to organic and low-spray commercial fruit operations. Current pest control measures rely on insecticides. These control measures are effective for now but long term management of the pest requires better understanding of the demography and history of the beetle. I'm using a variety of evolutionary biology methods to investigate and contribute to attempts to control this important crop pest.
Plum curculio (Conotrachelus nenuphar Herbst)
A major crop pest in the United States
Weevils cause damage to many of our most important crops. The plum curculio, Conotrachelus nenuphar Herbst, is one such weevil. The plum curculio is native and endemic to the eastern United States. In the North, these adults represent the only generation each year and they spend the rest of the season feeding on fruit and foliage in anticipation of overwintering. Southern plum curculio will go through another generation. The limits of the weevil’s distribution extend as far west as the 105th meridian, though records west of the 97th meridian are rare. The northern extent reaches into Canada and the southern extent falls just short of the Gulf coast.
Native hosts include hawthorn trees, crabapple trees, and the Chickasaw plum. After the introduction of domesticated fruit trees, the plum curculio began using crop trees as hosts. Now, its pest status well established, the plum curculio is a problem in commercial fruit production for a number of trees in the Rosaceae family—including plums, peaches, and apples. Accordingly, “it is the considered opinion of entomologists that plum curculios, not gravity, cause apples to fall” (Berenbaum 1991). In the eastern United States, plum curculio is an obstacle to organic and low-spray commercial fruit growing operations. Alternative control measures under development include nematode biocontrol and pheromone traps. Through the research discussed below, I am developing baseline demographic and genealogical information about this pest.
Population Genetics
Understanding pest population demographics
Using thousands of mitochondrial and nuclear base pairs across a handful of loci, I am investigating population subdivision and demographic trends of the plum curculio. In collaboration with more than a dozen agricultural research scientists, I have developed the most comprehensive and extensive tissue collection of plum curculio. These specimens are stored in liquid nitrogen at the AMNH's Ambrose Monell Cryo Collection. The genetic data generated from these samples is being treated by a variety of analyses, including statistical network analysis, phylogenetic analysis, DNA barcoding, genetic diversity indices, and analysis of molecular variance.
Preliminary results indicate significant genetic and geographical structuring of plum curculio subpopulations. Two disjunct COI haplotype networks have been recovered and broadly correlate with the north-south divide between the north-strain and southern-strain plum curculio. However, two northern populations clustered with the southern populations, indicating either the existence of multivoltive haplotypes in the north or lack of complete haplotype separation. I'm growing the dataset currently in order to clarify this issue. I'm also profiling the populations in anticipation of completing DNA barcodes for the species and (potentially) strains.
Niche Models
Predicting suitable habitat in quarantine zones & testing biogeographic scenarios
Environmental niche models (ENM) profile suitable habitat by correlating data about the environment (e.g. temperature, precipitation, soil type) at locations where the species is found. The ENM then allows for discovery of unsampled areas with suitable habitat. Preliminary results show a tight correspondence between the species distribution and areas predicted to be suitable. Using the results of the population genetic studies, I am building niche models based on a suite of different data partitions and using these models to explore the effects of genetic variation on model performance. Already it is clear that the northern and southern populations make different predictions when modeled separately. If additional study corroborates this result, the plum curculio ENM may have important implications for management plans. I'll also be using these niche models to find areas of suitable habitat in the western US and in countries that have listed plum curculio as a quarantine pest. These models may be useful in efforts to identify areas of potential invasion and prioritize monitoring programs.
Systematics
Discovering relationships & describing diversity
Conotrachelus is a New World genus with approximately 1 200 named species, primarily in South America. In the United States and Canada, there are approximately 60 named species. There is much undescribed, undiscovered diversity. Fiedler and Schoof both treated the genus in the 1940's. Fiedler focused on the South American members and produced the largest key to date. Schoof's treatment was much more restricted, concerning 23 species in the north-central US. There hasn’t been a systematic analysis of the genus since 1942. I'll be working in a nested fashion to scaffold up a phylogenetic analysis of the genus. I'll first and foremost be testing sister species status of the plum curculio and four or five very similar species (C. juglandis, C. buchanani, C. albicinctus, C. iowensis). From there I will test Schoof's classification of 23 North American species. The final goal is a representative total evidence dataset testing Fiedler's classification.
For this work, I am collaborating with Hector Barrios (Universidad de Panama) and Sara Pinzon Navarro (Natural History Museum, London). We will be using a combination of museum and fresh collected specimens. I currently have museum specimens on loan from Charlie O'Brien for all but a couple species from the US and Canada. I will be attempting to get DNA from these samples in 2009. If successful, I will expand my sampling and being work on the genus-wide analysis.
Completed Research Projects
Renibacterium salmoninarum Genome Project
Renibacterium salmoninarum, a gram-positive bacterium, is the causative agent of bacterial kidney disease (BKD) in salmonids. Bacterial kidney disease is characterized by lesions of the kidney and has a very high mortality rate. It occurs worldwide among wild and commercially raised fish populations, as well as in captive broodstocks of endangered species. Currently there are no effective preventative treatments. The aim of the project was to sequence the R. salmoninarum genome and use this data to identify targets for novel treatments that will attenuate the role of this pathogen as a limiting factor in salmonid culturing (Ponnerassery et al 2007, Wiens et al 2008).
As lead annotator of the draft genome, I manually inspected and annotated >1400 potential genes. I characterized several classes of genes that are especially promising targets for future treatments, including: macrolide and multidrug secretion proteins (an antibiotic resistance mechanism), signal peptide containing proteins (the targeting signal for attachment to the cell wall), and a sortase enzyme (responsible for the covalent attachment of surface exposed proteins to the cell wall). I discovered an intact sortase enzyme and successfully identified all of the genes that potentially encode sortase substrate proteins (Ponnerassery et al. 2007).
My findings were used to identify upregulated genes in antibiotic resistant strains of the bacterium (Ponnerassery et al. 2007). This is the first step towards the development of novel treatments that may result in the abatement of bacterial kidney disease. Such a development will have significant impacts on commercial fisheries and salmon conservation programs.