Part of Bia’s PhD project was the analysis of HAR1 evolution. HAR1 is the fastest evolving sequence in the human genome and is part of two overlapping long non-coding RNAs. Bia’s paper “Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1” describes in which order the 18 human-specific substitutions occurred and how they gradually changed the secondary structure of HAR1 into its human-specific form. She found that HAR1 is becoming more stable during human evolution. Her analysis methods are implemented in the software “MutationOrder”, which is publicly available and can be used for exploring the evolution of other RNA structures.
This project was a collaboration with Dan Tulpan. He won the Biovis design contest on visualizing RNA structure evolution that we co-designed at the ISMB conference in 2015. He joined our project after the contest and provided valuable visualization and scientific input to our paper.