Yes, it's always under construction...

Present Research

Evolutionary Ecology of Viruses

I am interested in theoretical topics of virus evolution. In particular the selective forces that determine evolutionary change in these 'organisms'. Viruses are capable of very rapid adaptive evolution in response to the multi-dimensional environments in which they exist. The reproductive requirements of most viruses result in the occupation of intrahost, interhost, and sometimes intravector selective venues which give rise to different, often conflicting adaptations and phenotypes. For instance, intrahost competition between viral strains may select for an increasing rate of 'consumption' of the host as reproductive substrate. However, while increasing progeny production may enhance the transmission probability of a strain from the host, the long term effect may be overexploitative and thus result in a decrease in the survival of potential new hosts. Therefore viral adaptations which increase fitness in one selective environment may actually decrease fitness in another.

Evolutionary Ecology of Human Papillomavirus

My empirical dissertation research involves examination of cervical samples taken from a population of mostly Native American women in Oaxaca, Mexico who, like women in many developing nations exhibit high rates of cervical cancer. Infection with human papillomaviruses (HPVs) is the primary cause of this disease. To date, over 100 distinct types of papillomavirus have been discovered and HPV infection is the most common sexually transmitted disease in the world. From an ecological standpoint HPV infection is quite extraordinary in that for a given human population many different types of HPV are simultaneously being transmitted from host to host at any given time yet only a single "habitat" exists (the human cervix). An evolutionary ecological explanation of this commonly observed diversity is one goal of my research.

To this end I am currently determining the distribution and exploring the molecular divergence of HPV types residing in the Oaxacan population. So far 26 HPV types including 1 previously unknown papillomavirus have been found. In addition I am examining the adaptive molecular evolution of HPV-16 E6 and E7 genes with special reference to T-cell epitopes and functional regions within these proteins. These are oncoproteins that are (exclusively) responsible for cell transformation. Despite their necessity for HPV replication they show unusual patterns of amino acid variation the potential causes of which I am examining. Finally I hope to conduct phylogenetic analysis of the HPV-16 haplotypes found in this population primarily to determine their place(s) of geographic origin.

Coevolution of Humans and Papovaviruses

Another empirical project that I am working on involves investigation of the past populational histories of human papillomaviruses (especially HPV type 6, 11, 16, and 18) and JC polyomavirus. Modern molecular population genetics theories allow very interesting hypotheses to be tested using genetic data regarding past evolutionary dynamics of organisms including demographic histories. Using large DNA sequence data sets I am investigating ancient changes in population size that have occurred in these viruses. Since small DNA viruses use mammalian host replication machinery for genomic dupilcation they exhibit relatively low mutation rates. Perhaps as one consequence of this they also rarely switch host species and have evolved reproductive lifestyles that involve low virulence and slow, persistent infection cycles. It has been demonstrated that many human populations have experienced large bursts in size during the past 30,000-100,000 years. To examine the role of the human host in the existence and evolution of these viruses I am looking for similar bursts in viral populations. If the viruses are extremely dependent on host population structure then we would expect diversification patterns in viral populations to mirror those seen in their human hosts.