Projects

Patterns of Gene Flow in the Bahamas--We have a currently funded project that is just getting off the ground to look at patterns of gene flow in the 6 species of bats that occur in the Bahamas. This project seeks to explore the extent to which narrow oceanic straits present barriers to gene flow. We are using a multi-locus data set to estimate changes in effective population size over time and patterns of gene flow. Coupled with the niche modeling data shown below, we can generate testable models of bat evolutionary history in the Bahamas using coalescent simulations. These simulations will allow us to determine which evolutionary models are most likely to produce the kinds of molecular data we observe in modern bats. This also allows us to predict how future climate change might affect Bahamian bat populations.

Caribbean Niche Modeling--Ecological niche models are routinely used to not only generate predicted distributions for species at the present time, but they are also used to generate past species distributions (e.g., those at the last glacial maximum). There has been a disturbing absence of testing to determine the degree to which these models accurately predict the past distribution of species. We are using the bat species of the Bahamas as a test case whereby we are generating predictive models of species distribution using various methods and testing their accuracy based on the fossil record of bats from the Caribbean. This study involves considerable field collection, computational effort (niche modeling), and molecular data analysis (to define taxonomic boundaries for niche modeling).

Ecological Niche Modeling of Widely Distributed Species--The modeling of widespread species is problematic due to high rates of omission errors in predicted distribution models. One potential source of error for such models is the fact that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We are testing niche models for the widely distributed oldfield mouse, Peromyscus polionotus because this species consists of numerous subspecies, some of which are ecologically or genetically distinct. We are finding that building ecological niche models based on smaller, biologically relevant subspecies (or populations) can provide much more accurate predicted distributions for the species as a whole. The use of molecular data can determine biologically relevant data partitions for modeling the distributions of widely distributed species.

Endosymbiont Genomics--Bacterial symbionts have allowed insects to radiate into niches with nutrient poor diets that otherwise would be unsustainable for insects. One example is obligate blood-feeding on mammals. Mammalian blood lacks vitamin B, and so insects that feed exclusively on mammal blood require endosymbiotic bacteria that synthesize vitamin B for their insect hosts. The sequencing of the human body louse genome uncovered a small plasmid (right) that contains the pathway for pantothenate (vit B). It could be a highly efficient way of assisting the insect host. Lice are peculiar in that each louse group seems to have a different endosymbiont lineage. Perhaps this plasmid makes it easier for any bacterium to function as a symbiont thereby facilitating endosymbiont replacement over time. This is one project that we are actively investigating now.

Mummy lice--Along with a long list of collaborators we have been able to sequence a small stretch of DNA from lice that are over 1,000 years old! These lice came from two well-preserved mummies from Peru, and they have the potential to tell us much about the peopling of the Americas. We are now seeking additional lice from New World mummies to continue this research. The first manuscript based on the ancient DNA sequence data appeared online in Journal of Infectious Diseases.

Florida Panther Research--The FLMNH receives all of the Florida Panthers that are found dead from various causes (e.g., hit by cars, male/male agression, etc.). Therefore, we have an amazing resources of over 100 FL Panther specimens that we can use to address various questions about diet and health. We have examined the osteopathologies that these cats suffer from (likely the result of severe inbreeding) to track changes in severity and prevalence over the past 50 years. We have also used stable isotope geochemistry to examine panther diet, which seems to vary in ways that we didn't expect. This work has been submitted to the Florida Museum of Natural History Bulletin. Check the web site in the summer of 2007 to find this work.

Tripartite Coevolution--We have recently been funded to study the shared coevolutionary history of mammals, their ectoparastic sucking lice, and endosymbiotic bacteria that live within the lice. It was previously thought that lice were able to radiate with their mammalian hosts due to the acquisition of an obligate endosymbiotic bacterium that allowed them to feed solely on mammalian blood (endosymbionts are required for obligate blood feeding). Sucking lice are found only on placental mammals, and they appear to have radiated roughly 65-80 million years ago (like placental mammals), so this previous hypothesis made a lot of sense. Shortly after the lice got a new endosymbiont, they radiated to fill a vacant niche alongside mammals. However, preliminary data show that the lice have acquired endosymbionts several times throughout their history, which begs the question “how often have these insects acquired obligate endosymbionts and where did they get them?” This project is ongoing and combines the interests of myself, Jessica Light (postdoc) and Julie Allen (Ph.D. student), and the project includes co-PIs and collaborators (Lance Durden, Vince Smith, Henk Braig, and Takema Fukatsu).

Louse genomics--Well, if you haven't heard yet, the human body louse genome has been sequenced and annotation is underway. You can keep up with the progress on the VectorBase web site. The data in the genome show that the body louse has a very compact genome, which is intriguing for many reasons. We are currently using the polymorphisms in the genome to find SNP-STRs and microsats that can be used for population level studies relating to human/louse co-demography studies. In the process of sequencing the human body louse genome, technicians were also able to sequence the whole genome of the endosymbiont as well. For our human/louse/endosymbiont work we now have full genomes for all three associates! This opens up amazing new avenues of research.

Population Genetics of the Florida Mouse--The Florida Museum of Natural History has an outstanding collection of the monotypic Florida Mouse thanks to the collecting efforts of Jim Layne and others. We will be looking at the population genetics of the historical populations sampled from within our collection, and our collaborator, James Austin, will be sampling current populations for comparison.

Rates of evolution in endosymbionts--Along with Dr. Braig's lab we are studying the elevated rates of nucleotide substitution in lice and their endosymbiotic bacteria. Lice are known to have faster rates of nucleotide substitutions than their vertebrate hosts (generally 3-5 times faster), and Nancy Moran and her colleagues have shown elevated rates of substitution in endosymbiotic bacteria. Does that mean that louse endosymbionts should be incredibly fast evolving? You'll have to wait to hear the answer, which is a manuscript in preparation.

Primary endosymbionts of Pediculus humanus--Several recent and forthcoming manuscripts have resulted from a collaboration between my lab and that of Dr. Henk Braig in Wales. Julie Allen (Grad student, Reed Lab) traveled to Dr. Braig's lab to take early DNA sequence data and create oligonucleotide probes that allowed us to determine that our DNA sequences were indeed from the mycetome-bound bacteria that were originally seen over 300 years ago. These endosymbionts reside in several distinctly different chambers (mycetomes) throughout the life of the louse, and the bacteria undergo two extracellular migrations. You can read about this work in our paper in the journal FASEB.

Endosymbionts of primate lice--A continuation of our work with Dr. Braig (see above) allowed us to sequence the 16SrRNA gene from human head lice, human body lice, chimpanzee lice, and human crab lice to confirm that these endosymbionts represent a monophyletic lineage of gamma proteobacteria. This work was published in Applied and Environmental Microbiology. You can find the sequences in Genbank, and the data matrices and trees in TreeBase.

How humans got pubic lice--Yes, you read the title correctly. Humans have two genera of lice (Pthirus, the pubic louse, and Pediculus the head or clothing louse). Chimps have a species of Pediculus (P. schaeffi) and gorillas have a species of Pthirus (P. gorillae), yet we have one of each (Pediculus humanus and Pthirus pubis). These lice are highly host specific, which begs the question "why do we have both?" It turns out that we have had Pediculus humanus throughout our history, and it diverged from the chimp louse species around 5.5 million years ago (just like the hosts did). The two Pthirus species on the other hand, diverged only 3.3 million years ago, which based on cophylogenetic analyses, means that we got our pubic lice from gorillas in a host switch. You can read more about this in our paper in BMC Biology (open access publication). See write-ups at Science Now, the NY Times, and The Loom. Hear Quirks and Quarks broadcast in MP3. You can get the sequences from Genbank and the data matrices from Treebase.

Close Contact Between Early Humans?--The head lice that parasitize living humans show much greater genetic diversity than do their human hosts. The three lineages of mitochondrial DNA found among head lice last shared a common ancestor over two million years ago, whereas the mitochondrial DNA of their human hosts coalesce much more recently (~150,000 years ago). We postulated in our 2004 PLoS paper that one of the louse lineages may have originated on an archaic species of human only to jump onto modern humans relatively recently. Coauthor Vince Smith has a web page that lists much of the public press that this paper received including articles in the NY Times, Washington Post and many others.