Shotgun sequencing and analysis of the extinct Conuropsis carolinensis (Carolina parakeet)

As the only neotropical parrot that lived in recent times in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 (Elphick et al. 2010). The cause of extinction remains contentious; besides excessive mortality associated to practices such as habitat destruction and active hunting, they could have been decimated by having a more patchy distribution range than previously thought (Burgio et al. 2016), or by being exposed to poultry pathogens (Snyder et al 2004, Snyder et al 2006). In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxic, carboxyatractyloside (CAT) (Stuart et al 1981), which did not seem to affect them but made the birds notoriously toxic to most predators (Snyder 2004). To explore the demographic history of this bird we have generated the complete genomic sequence of a preserved specimen held in a private collection in Spain, as well as the genome of its closest living relative, Aratinga solstitialis. Our analyses identified non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxic. Although our genomic analyses revealed evidence of a long-term demographic decline in the Carolina parakeet, its genome did not exhibit the long runs of homozygosity, that have been found typical signals of recent inbreeding in other endangered species. As such, our results suggest its extinction was an abrupt process, and thus likely solely attributable to human causes.