Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

Abstract

Predicting the genetic consequences of population decline is a major problem in conservation genomics. The black abalone was a culturally and economically important North American mollusk that declined by ~99% in the 1980s due to a rapid disease outbreak. To investigate the consequences of this event, we sequenced ancient genomes from shells spanning the past 1,500 y, producing the first population genomic dataset derived from this data type. This time-series data show that genomic impacts from this near-extinction event are extremely limited and that natural selection has acted recently on genes related to immunity. Together, these data are encouraging for the genomic future of this species and provide practical insight for how to manage recovering populations. Keywords: genomic erosion, local adaptation, temporal genomics, conservation, ancient DNA