• Calendar

December 18, Tuesday
12:00 – 13:00

High throughput DNA sequencing has transformed the landscape of genomic data by providing an affordable means to sequence the genomes of numerous species and multiple individuals per species. There has been a particularly dramatic increase in the last five years in the availability of individual human genomes and the genomes of closely related primate species. These data provide a rich source of information about human evolution and the forces that helped shape the human genome. This talk will focus on two specific problems I explored during my postdoctoral research using these new data sets.

The first problem I will be presenting is recovery of ancient human demography and the evolutionary relationships between different human population groups. I developed a new method, called G-PhoCS (Generalized Phylogenetic Coalescent Sampler) to infer demographic parameters along a population tree, and applied this method to the complete genomes of six human individuals from major human population groups. This approach allowed us to recover very ancient trends in human demography dating back as far back as 130 thousand years ago. The second problem is that of inferring signatures of recent natural selection acting on regulatory elements in the human genome. Much of the DNA in the human genome is devoted to the regulation of gene expression, but regulatory DNA elements are typically short, dispersed and often not conserved across long evolutionary timescales. This has made it very difficult for researchers to study the selective constraints that act on regulatory DNA in the human genome. I developed a method, called INSIGHT (Inference of Natural Selection from Interspersed Genomically coHerent elemenTs), that addresses these challenges by making use of individual human genomes and the genomes of closely related primates. This method was used to perform the first comprehensive study of natural selection acting on transcription factor binding sites, which are the most well characterized regulatory elements in the human genome. Our study sheds light on the selective forces that shaped these elements, and has possible implications to the study of human disease.

This talk will highlight the methodological and algorithmic challenges in these problems, and will not require any prior biological knowledge.