Phylogenetic Trees

Here are two of the trees I made from the data Dr. Miller gave me. The trees were both constructed on the program Mesquite. One tree was made with the PaupRAT algorithm, and the other was made with the RaxML algorithm. 

PaupRAT tree

RaxML tree

As you can see, the two trees vary pretty significantly. Different algorithms interpret the same data in different ways, which is why it is necessary to construct and compare multiple trees from the same data. At this point, we haven't done much analysis, and in the coming weeks, I'm going to construct and look at some more trees before Dr. Miller and I make any conclusions.

Avian Mycobacteriosis

Dr. Miller and I are using phylogenetic analysis to determine whether "avian mycobacteriosis" (which is basically an infection in birds) comes from the environment or is transmitted from bird to bird.

Avian mycobacteriosis affectes all bird species, and has a relatively low prevalence in captive species (1.2%). The prevalent belief is that this bacteria is transmitted from bird to bird via fecal contamination. If one bird in a population is affected by avian mycobacteriosis, then zoos generally euthanize the whole population. However, this practice has had several negative consequences, including a decrease in genetic diversity, and a decrease in effectivity of breeding and conservation programs.

Dr. Miller and I are working with a team in San Diego to determine whether the belief that the disease is transmitted from bird-to-bird is even correct. If the source of the infection is the environment, then there's actually no point in killing all of the possibly exposed birds. We're going to look at the similarities between the different strains of the infection observed in birds-- if the strains are nearly identical, then we can confirm a bird-to-bird transmission. His work with Peggy last year resulted in pretty convincing evidence that it wasn't, and now Dr. Miller and I are working with additional genetic data to either confirm or fail to confirm last year's results.

In the past, genetic samples have been taken from fingerprinting methods, which includes the RAPD method (gel banding pattern analysis, which is less reproducible and comparable), and the MLST method (captures 0.1% of a bacterial genome). We're working with whole genome sequencing, which is much more reliable and reproducible, although it takes more time to complete.

The data we've looked at so far has been supportive of an environmental source in most of the observed enclosures, but the results aren't completely conclusive. In the time we have left, we're going to construct additional phylogenetic trees with the new data to more accurately determine the source of the infection.