Still ruffling feathers after all these years: Darwin's finches and a molecular view of adaptive radiation

One of the many lovely things about molecular ecology is its ability to shine new light on old stories. The well-known case of Darwin’s finches is a classic example of adaptive radiation. These finches demonstrate a clear instance where over time, one species diversified into several that are adapted to different environments, or more specifically, food sources. In a nutshell (or maybe I should say seed), “Darwin’s finches” include 14 species that descended from those that first colonized the Galapagos about 2 million years ago, all with distinct beak shapes and sizes that allow them to eat different foods.
In the most recent cover article from Molecular Ecology, Chaves and colleagues dig deep into the morphological and genomic variation among three sympatric Geospiza species found in El Garrapatero on Isla Santa Cruz in the Galapagos. While genome-wide association studies (GWAS) are popular in many model systems, the authors state that these three species represent the finest branches on the evolutionary tree, suggesting that the “genomic architecture of their adaptive traits should reflect the variation actively shaping – and being shaped by – natural selection”. Basically, these birds are diverging and adapting before our very eyes, and present a good opportunity to study evolution in action.

Chaves et al., (2016) Figure 1. This paper is cool because it neatly combines traditional methods, including the careful measurement of morphological traits (like body size, wing length, and beak shape) as well as the relatively new method, restriction site-associated DNA sequencing (RAD-Seq). Briefly, for RAD-Seq, DNA is digested with a restriction enzyme, then the resulting sticky-ends of the fragments generated are bound to an Illumina flow cell and sequenced, allowing for the sequencing of genetic markers randomly distributed across an entire genome, perfect for GWAS.
figure2It’s all ’bout the beaks, so their primary goal was to find areas of the genome associated with the beak size of the bird (here, the adaptive trait).  Specifically, they identified single nucleotide polymorphisms (SNPs) using RAD-Seq, and determined which appeared to be linked to different beak sizes.

“If we are to understand the process of adaptive radiation, we must study its continuing action, as opposed to only examining well-established lineages that specialized in the distant past…”

figure4Chaves et al. found that the SNPs they identified explained the vast majority of beak size variation. Using the combo of morphological traits and sequence data, they confidently identified eight SNPs that predicted beak size, as well as an additional three correlated to beak and body size.Amazingly, it appears that out of all the SNPs they found (more than 32,000!), a small subset (~0.03%) are responsible for most of the variation. The SNPs were located on different chromosomes, and often (but not always) near genes previously found to be related to beak size.

“Because selection on beak traits is the key mechanism driving evolution of the entire group, analysing this sympatric continuum should inform the genetic architecture associated with the process of (ongoing) adaptive radiation.”

For us non-finch experts, the authors also give a brief summary of how this work relates to other studies on the topic. Additionally, the succinct perspective by Mundy included in this issue is a nice overview of the article. It’s amazing that just a handful of SNPs seem to be responsible for such distinct adaptive traits as beak shape. I guess in the end the authors present a good example of how both sequencing and traditional methods are actually, for the birds. (sorry, couldn’t help myself)
Chaves, J.A., Cooper, E.A., Hendry, A.P., Podos, J., De León, L.F., Raeymaekers, J.A., MacMillan, W.O. and Uy, J.A.C., 2016. Genomic variation at the tips of the adaptive radiation of Darwin’s finches. Molecular Ecology. doi: 10.1111/mec.13743
Mundy, N.I., 2016. Population genomics fits the bill: genetics of adaptive beak variation in Darwin’s finches. Molecular Ecology, 25(21), pp.5265-5266. doi: 10.1111/mec.13868

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