DETECTING PUNCTUATED EVOLUTION IN SARS-COV-2

SARS-CoV-2 evolved slowly over the first year of the COVID-19 pandemic, with different mutation rates across lineages. How did this variation arise? Using phylogenetic regression models, we show that ~13% of SARS-CoV-2 genomic evolution up to May 2020 is concentrated at lineage branching events (i.e., punctuated evolution). This small punctuational contribution to SARS-CoV-2 diversity is consistent with the 'founder effect' resulting from narrow transmission bottlenecks. Therefore, punctuation in SARS-CoV-2 may represent the macroevolutionary consequence (rate variation) of a microevolutionary process (transmission bottleneck).

FOSSIL RECORD BIAS IN MACROEVOLUTIONARY ANALYSES

Fossil record bias confounds analyses of species dispersal through space and time. Circa 400 million years ago, fish-like ancestors of tetrapods, four-limbed vertebrates, moved from water to land. Using this transition as a case study, Jacob Gardner, Chris Organ, and I propose a proxy for fossil sampling bias that incorporates geographic information. We initially found that the water-land transition occurred in Euramerica and that cross-continent dispersals tend to be rapid. However, these results are unreliable because they can be explained by insufficient fossil record in all regions except Southern Euramerica.

BIRD TAIL DEVELOPMENT AND EVOLUTION

Pygostyle. The long tail of Mesozoic dinosaurs rapidly evolved into the short, terminally-fused tail of living birds. Two fossil specimens (Zhongornis haoae and the dinosaur tail preserved in Burmese amber) exhibit a transitional tail morphology: short and unfused. However, our study on bird tail development warrants re-interpretation of these transitional species. Bird tail vertebrae change radically with growth. As birds reach maturity, the last four to six vertebrae fuse into a compound bone called the pygostyle. Vertebral side projections mineralize long after hatching. Zhongornis, as a juvenile, might not have yet formed a pygostyle, and the dinosaur tail, also immature, might be avian.

Pygostyle Development. My colleagues and I found that vertebral fusion in bird tails is driven by sterile inflammation and resembles bone fracture repair. This finding demonstrates a role for inflammation in skeleton development. The immune system is involved in pathological bone fusion, but we also found it to be a crucial contributor to normal vertebral fusion. Evidence of necroptosis indicates that this type of cell death can occur in post-birth development. Moreover, we documented nucleus pulposus structures in tail discs in birds. Lastly, corticosteroid treatment inhibits vertebral fusion, suppressing a Cretaceous avian flight adaptation while demonstrating an unreported effect of corticosteroids on skeletal maturation.

Spinal Nerve. Ground-dwelling birds like the emu and kiwi (paleognaths) have holes in their pygostyles. These holes are absent in other birds' pygostyles (chicken, Chinese quail, and rock dove) or the tail vertebrae of the brown anole and American alligator (close living relatives of birds). What is the purpose of the holes? My colleagues and I study the tail development in the species above and found that the paleognath spinal nerves uniquely extend to the very end of the tail. The holes seem to serve as exit points for these nerves. Looking back through time, we find that these holes also exist in the Mesozoic confuciusornithids, extinct relatives of modern birds, indicating an ancient origin. The paleognath unique nerve configuration, combined with other evidence such as the likely independent gain of pygostyle in the extinct bird Fukuipteryx prima, spitballs yet untested speculation: Living birds arose from more than one long-tailed ancestors.