PRJNA481495
The genomic Footprints of the Fall and Recovery of The Crested Ibis
How the genomic diversity of endangered species is shaped by their interactions with the environment and other direct human actions is a fundamental question in conservation biology. Typically, such efforts have focused on present day samples, thus represent the end product of such interactions. However, to provide temporal context, a growing number of studies have begun to include small numbers of genomic loci extracted from historic and even ancient specimens. We extend such approaches to their natural conclusion, by characterizing for the first time the complete genomic sequences of both modern and historic population samples of an endangered vertebrate, the crested ibis (Nipponia nippon). Although the contemporary population's size has recovered from its historical low of only seven individuals, following three decades of intensive conservation efforts, we find its overall genetic variation is only 53.50% of that of historical populations, and that it today suffers from an extremely high deleterious mutation load. We furthermore show how genetic drift following the population bottleneck coupled to inbreeding have largely purged the ancient polymorphisms from the current population. Furthermore, we find a rapid occurrence of new derived mutations particularly in protein-coding regions following the establishment of the recovery breeding program, with ca. 780 SNPs per generation. In conclusion we demonstrate the unique promise of exploiting the genomic information held within museum samples for conservation and ecological research.