Deep-Time Paleogenomics

Fully understanding any system in biology includes understanding how that system evolved, and that is the domain of macroevolution. For example, our understanding of the sequence, rate, and direction of morphological evolution across the breadth of life is empirically founded on fossil evidence – a crucial dataset that is absent in genome biology (with the exception of recently extinct species). Extant species represent a scant 0.01% of all species that have ever lived, a tiny sample from which to understand genome biology and evolution. If we can leverage data from the other 99.9% to better understand genome biology, even if incomplete, we must do so. A primary research objective in our lab is to integrate genomics and paleontology with computational biology so that, like morphology, the fossil record can yield insights into how and why genomes evolved.

MarmorerpetonWe are currently studying urodeles (salamanders and newts), which have the largest genomes among extant tetrapods. The evolutionary tempo and mode of genome size expansion in urodeles is poorly documented because genome size varies substantially among urodele taxa and because genome size does not directly fossilize. Because all urodeles have large genomes compared with other extant tetrapods, their last common ancestor, which lived at least 168 Ma ago, likely already had a large genome. We are using histological data from a Middle Jurassic (Bathonian, 166–168 Ma) urodele  (one of the oldest known stem-urodeles) to find out when salamander genomes expanded.