Evolutionary history, genomic adaptation to toxic diet and extinction of the Carolina parakeet
As the only endemic Neotropical parrot to have recently lived 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 its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy (Burgio et al., 2017), or by the exposure to poultry pathogens (Snyder, 2004; Snyder and Russel, 2002). In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or 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 generated the complete genomic sequence of a preserved specimen held in a private collection in Spain, as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process, and thus likely solely attributable to human causes.
Steps to reproduce
See commands_and_data_structures.pdf to reproduce results and for an explanation of the files given. The file explains the commands, input and output files to reproduce the UCE phylogenomics pipeline, maximum likelihood tree search and the fossil calibration analysis. The folder mitochondrial_data/ contains the files needed to run the calibration analysis from the mitochondrial genomes.