Christina Bergey - Projects
Rainforest Hunter-Gatherer Adaptations
My current main project uses population and functional genomic techniques to investigate human adaptations to life in the rainforests of Africa, a challenging environment for its human inhabitants. One such adaptation is the evolution of small body size (the 'pygmy' phenotype) in rainforest hunter-gatherers. Working with populations in Uganda, we are using a comparative approach that combines population, evolutionary, and functional genomics to better understand critical human growth and development pathways using this natural human model of small body size. This research is funded by a grant from the National Institutes of Health to George Perry (PSU) and Luis Barreiro (CHU Sainte Justine, Université de Montréal).
Anthropoid Evolutionary Genomics
With Andrew Burrell and Todd Disotell at NYU, we are using genomic data to explore the evolution of anthropoid primates (New World monkeys, Old World monkeys, and apes). As part of an NSF-funded project, we are sequencing the genomes of approximately 36 primate genera for which little or no such data are available. This comparative data will allow us to identify regions of the genome that may influence important adaptive traits of major monkey and ape lineages, including what is unique about the human genome. Additionally, we will be able to infer a reliable evolutionary tree of anthropoid primates, and estimate the timing of the origins of major primate lineages. This research will result in a freely accessible anthropoid primate genomic database.
Methods for Genomics from Non-Invasive Samples
Kenny Chiou (Washington University in St. Louis) and I developed a method to inexpensively and easily purify host mammalian DNA from DNA extracted from feces. Feces is abundant, but the DNA it contains is mostly from the items in the diet of the host or the bacteria in its guts. Our method, which exploits the methylation differences between animal and bacterial DNA, makes it possible to enrich the host DNA and do population-level genomic analyses. It is particularly useful for species that are cryptic or endangered or otherwise difficult to trap or dart. A preprint of the FecalSeq method is available. For popular science coverage of the work, see this Gizmodo post.
Tapeworm Phylogeny and Functional Genomics
Much can be learned about human evolution by studying the evolutionary history of the organisms that parasitize us. We are studying the evolutionary history of tapeworms (genus Taenia) for insight into the origin of meat eating in hominins. The work is funded by a grant from the Wenner-Gren Foundation for Anthropological Research to PI George Perry (PSU).
Awash Baboon Hybrid Zone
For my Ph.D., I studied gene flow between two species of baboons in Awash National Park, Ethiopia. There, hamadryas and anubis baboons (Papio hamadryas and P. anubis) mate successfully, despite diverging hundreds of thousands of years ago and differing markedly in phenotype, behavior, and social structure. We found key differences in the dopamine pathway between the two species, published in Proceedings of the National Academy of Sciences. Commentary on our findings can be found here. To characterize the structure of the hybrid zone, I genotyped thousands of loci spread throughout the genome using the ddRADseq technique, a slightly different version of the one we previously applied to many primates.
I am currently testing a new method to sequence the MHC-DRB exon 2, a small fragment of the Major Histocompatibility Complex (MHC), in primates using the Illumina MiSeq platform in lieu of cloning.
RAD-seq in Primates
Restriction site-associated DNA sequencing (RAD-seq) is a new technique that allows inexpensive and fast discovery of thousands of markers in many individuals. I along with Andrew Burrell, Luca Pozzi, and Todd Disotell demonstrated its application in five primates and discuss its potential for primatology research. The report was published in the International Journal of Primatology.
Survey of Guenons in Democratic Republic of Congo
Inferring Primate Diet from Prey DNA in their Feces
Sarah Pickett, now of University of Washington, Tony DiFiore, of UT Austin and I completed a metagenomic study of New World primate diet diversity by amplifying arthropod DNA from platyrrhine feces. The study was published in the American Journal of Primatology.
Kinda Baboons in Kafue National Park, Zambia
For six weeks during the summer of 2011, I traveled to Zambia with Cliff Jolly, Jane Philips-Conroy, Jeff Rogers, Monica McDonald, and Kenny Chiou to study the little-known Kinda baboon (Papio kindae). A paper on the genetics of hybrid baboons in Kafue, which I worked on as an undergraduate, was published in the American Journal of Primatology.
AluHunter is a program for bioinformatic identification of potentially polymorphic Alu elements for use in primate phylogeny and population genetics. The AluHunter project website contains info on and primers for 42,055 polymorphic Alu elements, as of April, 2011. Over 1.9 million Alu elements have been screened. The database was published in the journal, Bioinformatics.