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Galapagos Finch Beak Size Locus Identified by Resequencing

NEW YORK (GenomeWeb) – Variants around a known growth gene contributed to beak size divergence in resource-limited Galápagos finches during a recent drought, new research suggests.

A team from Sweden and the US resequenced the genomes of 10 birds apiece from six small, medium, or large ground or tree finch species on the Galápagos island of Daphne Major. Results from the analysis, published this week in Science, support the notion that closely related species can take on divergent traits when competing for the same set of limited resources.

In particular, the researchers saw evidence that the medium ground finch, Geospiza fortis, became slightly smaller beaked to minimize competition with the large ground finch, G. magnirostris, with help from two haplotypes spanning the HMGA2 gene. That gene, which codes for a chromatin-related protein, has been implicated in everything from body size and/or height to cell type transitions that can lead to cancer.

"The HMGA2 gene regulates the expression of other genes, but the exact mechanism how it controls beak size in Darwin's finches or human stature is unknown," senior author Leif Andersson, a researcher affiliated with Uppsala University, the Swedish University of Agricultural Sciences, and Texas A&M University, said in a statement.

In the 2 million or so years since finch ancestors reached the Galápagos Islands, the birds have diversified into roughly 18 species with variable body sizes, beak features, dietary preferences, lifestyle habits, and so on, the team explained.

In a study published in Nature last year, Andersson and colleagues presented findings from a genome resequencing study exploring this adaptive radiation in 120 Galápagos finches from 15 species — an analysis that uncovered a genetic haplotype in and around the ALX1 gene that was varied in finches with blunt or pointy beak shape.

The latest study focused on beak size, using clues from finch species exposed to drought conditions just over a decade ago. The ecological character displacement theory, an updated version of a hypothesis first proposed by Darwin, holds that species are more prone to divergence from one another when they rely on a single food source.

The team suspected this was the case for medium and large ground finches, which went through a severe drought in 2004 and 2005. During that event, the medium ground finch beak appears to have become smaller, on average, distinguishing it further from the large ground finch.

The researchers re-sequenced 60 finches from six species on Daphne Major to around tenfold average coverage each, aligning the reads to a reference genome assembled for a medium ground finch.

Using the nearly 45 million variant sites detected in the genomes, they put together a phylogenetic tree for the newly sequenced birds and for 120 finches that were re-sequenced previously.

A handful of regions jumped out when the team searched for signs of genetic differentiation in the genomes, including a site spanning HMGA2 and three other genes. A closer look at the latter locus revealed two SNP haplotypes, one that was common to large birds and another that turned up in almost all of the small finches.

By genotyping more than 100 other finches, the team saw that variants in the haplotype seemed to have an additive effect on beak size, accounting for more than one-quarter of the beak size variance considered in the finches.

The smaller beak-associated haplotype dominated amongst medium ground finches that survived the drought, turning up in some 61 percent of 37 surviving birds. But it was less common in a set of 34 medium ground finches that perished in the period of lower food availability, turning up in just over one-third of those birds.