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Program
Katherine S. Pollard, Department of Statistics and UC Davis Genome Center, UC Davis
Rapid evolution in the human genome
Comparative genomics is a powerful approach to investigating the genetic basis for what makes us human. I will describe two different methods we have developed for identifying lineage-specific evolution: a phylogenetic hidden Markov model (phylo-HMM) and a likelihood ratio test (LRT). The phylo-HMM works well for identifying relatively ancient events, while the LRT is much more powerful at the leaves of a phylogeny (e.g. the human lineage). Using this LRT, we recently identified 202 Human Accelerated Regions (HARs) that were extensively changed in the last ~6 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. The HARs are mostly non-coding sequences, and the set of genes near HARs is enriched for transcription factors, suggesting a role for HARs in the evolution of human gene regulation. I will describe a few of the most intriguing HARs before turning to a curious observation about the HAR sequences: the most accelerated regions show a striking bias for AT to GC ("weak-to-strong") nucleotide substitutions. This pattern is used to speculate about the cause of rapid, biased evolution in the primate genome and to date the chromosome fusion that formed human chr2.