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Finch Genomes Offer New Details on Adaptive Radiation Described by Darwin


NEW YORK (GenomeWeb) – A team from Sweden and the US used genome sequencing and phylogenetic analyses to narrow in on a transcription factor locus that contributes to the beak diversity that Charles Darwin famously noted amongst Galápagos finches.

As they reported online today in Nature, the researchers did whole-genome re-sequencing on 120 Galápagos finches spanning 15 species. From the resulting finch phylogeny, they refined relationships between the birds, identifying extensive gene flow between species and instances in which finch phenotypes had led to slightly skewed taxonomic assignments.

It also identified more than a dozen loci linked to beak shape. Among them: a haplotype in and around the transcription factor-coding gene ALX1 showing pronounced ties to beak diversity in the Galápagos finches in general and within the medium ground finch species.

"Natural selection and introgression affecting [the ALX1] locus have contributed to the diversification of beak shapes among Darwin's finches and hence to their expanded utilization of food resources on Galápagos," senior author Leif Andersson, a researcher affiliated with Uppsala University, the Swedish University of Agricultural Sciences, and Texas A&M University, and colleagues wrote.

Mitochondrial DNA data suggests finch radiation in the Galápagos archipelago occurred within the last 1.5 years or so, the researchers explained, producing 14 behaviorally and physically diverse species from a shared ancestor. A related species is found on the nearby Cocos Island.

In an effort to tease apart branching events during this rapid radiation, researchers used the Illumina HiSeq 2000 to do paired-end genome sequencing on DNA in blood samples from 120 birds that had been captured and released, generating 10-fold coverage of each genome, on average.

The re-sequenced representatives spanned all 15 finch species from the Galápagos archipelago and Cocos Island. The team did similar genome resequencing on tanagers from Barbados, which are related to the finches but distant enough from them to serve as a phylogenetic outgroup.

After aligning re-sequenced genome reads to the existing medium ground finch genome assembly, the researchers tallied up genetic diversity within and across the finch species, identifying some 45 million SNPs. They also used variant profiles to delve into everything from finch phylogeny to estimated population sizes over time.

By determining divergence times within the finch family tree, for instance, the team was able to estimate gene flow between the species over the course of their rapid radiation.

When they focused in on birds that were closely related but had pronounced beak differences, meanwhile, the investigators identified 15 potential beak-associated loci — a set that included at least half a dozen sites already implicated in head, face, and beak development in birds or other animals.

A stretch of 240,000 bases surrounding ALX1 showed the most marked ties to beak shape. Finch species with blunt beaks tended to share a homozygous ALX1 haplotype dubbed the "B" haplotype, for example, while pointy-beaked finches were typically homozygous for the so-called "P" haplotype.

The team found similar patterns when it profiled ALX1 genotypes in more than two-dozen more medium ground finches and compared them to other hybrid and non-hybrid finches. In that species, the pointed beak haplotype has became more common since the late 1980s, when a drought in the region altered the type of food sources available. 

"[G]enetic variation in the ALX1 gene is associated with variation in beak shape not only between species of Darwin's finches but also among individuals of one of them, the medium ground finch," Andersson said in a statement. "This is an interesting example where mild mutations in a gene that is critical for normal development leads to phenotypic evolution."