E&E Seminar Series - Characterising gradual and punctuated evolution using phlyogenetics

Abstract - The molecular clock hypothesis proposes that evolutionary change occurs as a temporally regular process, occurring at a rate that might fluctuate through time, but still remains more-or-less consistent. This framework forms the basis of phylogenetic clock models and divergence dating, based on a range of biological data types (DNA, protein, morphological traits, etc.). However, a gradualistic view of evolution cannot detect evidence for the scenario where macroevolutionary change is abruptly accelerated at the moment when one lineage splits into two; as described by the theory of punctuated equilibrium (Eldredge and Gould 1972). In reality, it is known that many biological systems do indeed evolve this way, e.g. certain cases of allopatric speciation or gene neofunctionalisation.

In this talk I will give an overview on my past six years of work on phylogenetic clock rate variation. I will describe the optimised relaxed clock (ORC) model and its role in species tree estimation under the multispecies coalescent model (StarBeast3). I will show how this approach is extended to capture punctuated evolution, demonstrating its use on three unrelated systems across different scales of life: cephalopod morphologies, aminoacyl-tRNA synthetase sequences, and Indo-European languages. I will present methods that describe a special case of sweeping punctuated change across the entire proteome, resulting from changes in the genetic coding alphabet during the earliest stages of life on Earth. Lastly, I will open the black box behind these biological processes, and explore drivers of molecular rate variation, demonstrated on mammalian body sizes.

Biography - Jordan Douglas studied bioinformatics and statistics in his undergraduate, before completing his PhD in Computer Science in 2019. As a research fellow at the University of Auckland, New Zealand, Jordan developed novel phylogenetic methods. At the start of the COVID-19 pandemic, he put these skills to the test by working with public health bodies to trace viral transmission in New Zealand in real-time. Since then, his research has largely focused on protein structural evolution and the origins of genetic coding through the lens of the aminoacyl-tRNA synthetases. In his current position as a postdoctoral researcher at the Research School of Biology here at ANU, Jordan studies the evolutionary drivers behind molecular rate variation.