links C V code research publications home bird

I am a bioinformatics scientist in the informatics group at Harvard University. My general interests include phenotypic evolution, phylogenetics, behavioral ecology, genomics, selection, and ornithology.

Allison with a Long-tailed Rosefinch in Mongolia

Allison holding a Long-tailed Rosefinch, a relative of the House Finch on a collecting trip with Harvard's Museum of Comparative Zoology to eastern Mongolia in the summer of 2012. With Scott Edwards, several members of the MCZ bird department, and a team of Mongolian ornithologists, she helped to increase the genetic resources and specimens available from that part of the world.

Phylogeography and Genome Evolution of the House Finch

As part of my PhD work, I used genomic tools to address questions about avian population genetics and evolution. My study system is the House Finch, an important species in behavioral and disease ecology. Native to the western United States and Mexico, this species was introduced to Hawaii and the eastern United States in about 1870 and 1940 respectively, where the populations quickly expanded. In 1994, the eastern population was colonized by the bacterium Mycoplasma gallisepticum. While upon first exposure this bacterium was deadly to House Finches, they have since evolved resistance and tolerance. This bacterium has now infected individuals from almost the entire range, and provides an opportunity to study what effect this strong selective pressure had on the genome.

I used using Rad-tag sequencing on historical samples to study the phylogeographic patterns of this species before exposure to the epizootic. Building upon this work, I am using whole genome resequencing of populations before and after exposure to MG to learn about the types of selection (hard sweeps, soft sweeps, etc) and identify innate immune pathways and genes that were targets of selection.

Dr. Scott Edwards
Dr. Geoff Hill

Avian Tetrahedral Color Space

An example of the (a) belly, (b) back, and (c) breast measurements of the Multicolored Tanager, plotted in the avian tetrahedral color space. The distance between male and female measurements are shown by lines drawn in between the corresponding male and female points, and the dotted line indicates the most dichromatic patch - the breast measurement.

Evolution of Tanager Coloration and Tanager Diversification

For my Master's research, I studied several aspects of tanager plumage coloration. The tanagers are a diverse group of 370 species that live throughout Central and South America. They have a wide variety of life histories, habitats, and plumage patterns. One of the underlying themes of my research was the use of the avian visual model. Birds see quite differently than we do, notably they can see UV coloration and can distinguish between colors better due to colored oil droplets on each of the cone cells. First, I used the avian visual model to assess the prevalence of cryptic sexual dichromatism - differences in male and female plumage coloration visible to birds but not humans. Second, I investigated whether it was changes in male or female plumage coloration that were driving the evolution of sexual dichromatism, and how male and female models of evolution differed. Finally, I looked for correlations between sexual dichromatism and different coloration mechanisms.

In addition, in collaboration with the lab of my Master's advisor, Kevin Burns (also known as Team Tanager), I helped to construct a species-level phylogeny of the tanagers. We will combine the phylogeny with data we have collected on tanager plumage coloration, songs, niches, and bills to look at how tanagers have diversified in relation to these phenotypic traits.

Dr. Kevin Burns
Nicholas Mason
Pascal Title

Centennial Resurvey of the UC Berkeley Campus Avian Community

For my undergraduate honors thesis in the lab of Rauri Bowie, I examined how the avian community of the UC Berkeley campus has changed over 93 years. Using survey data collected from 1913-1918, 1939-1940, and 2006-2007, I discovered that the species richness and functional diversity of the community had not changed over time. Furthermore, specialists were not replaced by generalists, as may be predicted. However, the community composition changed significantly between all three of the different time periods, with species in each time period that preferred the habitats presented by the landscaping at each time. The results of my research suggest that by landscaping native habitats, native bird communities can persist through time or be restored, even in developed areas.

Dr. Rauri Bowie
Dr. Morgan Tingley

A canonical variates analysis of campus species based on habitat preference. Species are colored by compositional changes through the time periods.

Allison using the spectrophotometer Campus Resurvey Figure allison j shultz