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African Genetic History Uncovered with UA Research Computing
African Genetic History Uncovered with UA Research Computing
UA professor Dr. Ryan Gutenkunst and graduate student PingHsun Hsieh

Throughout recorded history different groups of people have shared unique physical traits that were distinctive from their neighbors or later generations. For University of Arizona scientists researching these differences, learning when and where those traits developed increases our understanding of human genetic changes and adaptations over many generations.

UA Research Computing is helping these scientists by providing computing power that allows them to search data quickly and efficiently. UA professor Dr. Ryan Gutenkunst and his team in the Department of Molecular and Cellular Biology, in collaboration with Dr. Michael Hammer and his team in the Department of Ecology and Evolutionary Biology, use Research Computing resources, specifically High Performance Computing (HPC) systems, to attempt to unravel why some African tribes are so different from their neighbors. The team is tracking millions of genetic bases to infer changes eons ago that could result in today’s distinctive differences.

For example, in the rainforests of central Africa live about one dozen tribes whose members are remarkably small, on average just over four feet tall. Originally called Pygmy by early European explorers, these hunter-gatherers are much shorter than their nearby farming neighbors.

Generally, unique traits are the result of genetic drift, in which many random neutral changes accumulate, or adaptation, in which traits are advantageous given particular environmental influences such as food supply or climate change, or a combination of both. By modeling the history of Pygmies and their neighbors, Dr. Gutenkunst’s team can isolate the effects of genetic drift to test which traits, such as short height, that are unique to Pygmies are adaptive.

“The short term goal is to develop a model of history of these populations – hunter gatherer and agricultural populations – then match that model up with little bits of history that we already know,” Dr. Gutenkunst explains. “Once we have a model we can look back at genetics to eliminate theories that do not fit the model. We need the High Performance Computing to help search for the best model.”

To construct millions of possible models covering hundreds of human generations takes tremendous computing power. Fortunately for Dr. Gutenkunst’s team, UA’s Research Data Center is an invaluable resource. “Each model takes hours to run on a single computer,” says Dr. Gutenkunst. “Since we have many models to evaluate, the ability to use hundreds or thousands of processors at Research Computing is essential to our work.”

Dr. Gutenkunst says that investigating African demographic history is a key to understanding our species, because humans originated in Africa and Africa harbors more human diversity than any other region of the world. The genes that influence body size are likely to play important roles in common modern disorders, such as type-2 diabetes and hypertension. Understanding the genetic basis of these disorders may lead to further research on their care and prevention.

More information on the Africa project is available on the group’s website, http://gutengroup.mcb.arizona.edu

 

Disciplines across campus utilize Research Computing resources. The services are free of charge to any UA researcher with a need for HPC/HTC (High Performance Computing/High Throughput Computing) systems. The new Research Data Center opened in February 2012 with five HPC/HTC systems including an affordable buy-in option for projects requiring high priority computing time. For more information on how to gain access to these systems visit HPC/HTC Getting Started.