The genetic evolution of Darwin’s finches

Darwin’s finches are once again making scientists rethink evolutionary history. A genetic analysis of the finches reveals three new species. And the birds’ most iconic adaptation, beak shape, is largely controlled by a single gene, researchers report February 11 in Nature. That gene is also known to shape faces in mammals, including humans.

The analysis “is rewriting the taxonomy of these birds, and that’s a pretty big deal,” says Scott Edwards, an evolutionary biologist at Harvard University who was not involved in the work. “These birds are the epicenter of evolutionary theory.”

A common ancestor of most of the finches arrived in the Galápagos archipelago about 1.5 million years ago. One other Darwin’s finch species, the Cocos finch (Pinarloxias inornata), lives on Cocos Island off the coast of Costa Rica. The finches have fascinated people since Charles Darwin brought back specimens from a survey voyage of the HMS Beagle in the 1830s, and mentioned the birds in On the Origin of Species.

For the new study, evolutionary biologist Leif Andersson of Uppsala University in Sweden and Texas A&M University joined up with Peter Grant and B. Rosemary Grant of Princeton University, who have studied Darwin’s finches for more than 40 years. Their team sequenced the genomes of 120 birds, including several birds from each of the 15 known Darwin’s finch species and two species of tanagers, close relatives to the finches.

By examining the birds’ DNA, the researchers discovered the genetic underpinnings of the finches’ beak shape. The ancestor of the finches probably had a pointy beak, but some of the species developed blunt beaks better for crushing seeds. In the new analysis, the researchers found that blunt beaks are associated with a new form of a gene called ALX1. That gene is also known to control facial development in people.

The big effect ALX1 alone has on beak shape may surprise many researchers because other complex traits, such as height, are known to be controlled by many genes, each with a tiny influence, says Richard Gibbs, a human geneticist at Baylor College of Medicine in Houston. But “data trumps expectation,” he says. “There is a clear, loud bell being rung here that a morphological trait like beak shape can be driven by a simple, strong genetic effector.”

The researchers also uncovered clear evidence that the different forms of ALX1 may help birds adapt to their surroundings. Medium ground finches (Geospiza fortis) on the island Daphne Major started to develop pointier beaks after a drought in 1985 and 1986. Pointy beaks may help the birds reach seeds that have fallen into cracks in rocks.The team found that the blunt-beaked G. fortis finches had inherited the pointy version of ALX1 by hybridizing with small ground finches (G. fuliginosa) and common cactus finches (G. scandens).

Hybridization also played a big role in creating several new species of finch, the team found after constructing a genetic family tree of the birds. Like trees based on the way the birds look, or their morphology, the genetic tree suggested that warbler finches were the first to branch off, about 900,000 years ago. Ground and tree finches began rapidly branching into new species about 100,000 to 300,000 years ago. But the team found a few surprises, too.

Scientist thought that sharp-beaked ground finches (G. difficilis) from six different islands shared a single common ancestor. But the new data indicate that the birds are probably three species, each with its own ancestor. One of the new species resides on Pinta, Santiago and Fernandina islands, a second on Wolf and Darwin islands, and a third on Genovesa Island.  The new species may be a product of hybridization. The Wolf and Darwin finches, for instance, get most of their ancestry from large ground finches (G. magnirostris), but may have inherited their defining physical characteristics through interbreeding with G. difficilis.

Similarly, the large cactus finch (G. conirostris) is actually two species — a blunt-beaked species that lives on the island of Española and a pointy-beaked variety from Genovesa Island. The birds from the two islands have been interbreeding, perhaps accounting for their resemblance to each other.

These findings are somewhat surprising, as scientists have thought that species cleanly branched from each other, Edwards says. The new results suggest that hybridization may be important for giving species genes that help them adapt to new environments or food sources.