Population Genomics of Passenger Pigeons

The passenger pigeon was once the most abundant bird in North America, with flocks that, during the early and middle 19^th century, were estimated to comprise up to three billion individuals. Less than 100 years later, however, passenger pigeons were extinct.  To test the hypothesis that over-exploitation drove passenger pigeons extinct, and to explore the genomic consequences of rapid population decline, we sequenced and assembled 41 mitochondrial genomes and five high-quality nuclear genomes from passenger pigeons and, using new technologies for de novo genome assembly from Dovetail Genomics, a nuclear genome from band-tailed pigeons (the closest living relative of passenger pigeons). Our mitochondrial data indicate that passenger pigeon populations were growing exponentially at the time of their extinction and not in a period of decline. The nuclear genomic data reveal a striking, bimodal genomic pattern of genetic diversity with regions of extremely high and low diversity organized in distinct segments across the genome. We hypothesize that this pattern is a consequence of a long-term extremely large effective population size and consequent dominance of natural selection as an evolutionary force.