Researchers combined whole-genome data with measurements of morphology in Camarhynchus tree finches, which diversified during the past 100,000 years. The birds show marked physical differences even though their genomes are otherwise only shallowly separated.

The team identified several highly differentiated genomic regions, including G03, a supergene associated with beak and body size. In two species living in the same area, most of the genetic difference between them was concentrated at G03, while different forms of the region appear to have diverged early in the group’s evolution.