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The genomics of Darwin’s Finches by Luke Musher

Once again we have the chance to let the MA students present a critical reading of a new paper. In this case the show is run by Luke Musher. Take it away Luke…

A recent (2014) paper in Nature entitled, “Evolution of Darwin’s finches and their beaks revealed by genome sequencing” by a group of authors including Peter and Rosemary Grant, and a number of researchers in Sweden, sequenced the genomes of Darwin’s finches in order to better understand the history of the radiation in this model system for evolutionary biology.

There are 15 species of Darwin’s finches, 14 from Galápagos and 1 from Cocos Island off the coast of Costa Rica, and are actually not finches at all, but are in the tanager family. This group has been one of the most important and most referenced systems in evolutionary biology because the radiation of this diverse group happened quickly over the past 1.5 million years, because the radiation is relatively intact without any anthropogenic extinctions, and because natural selection is thought to have played a major role in the group’s diversification.

The authors sequenced the genomes from a total of 120 individuals, including all three species throughout the islands, built phylogenetic trees, and searched for evidence of gene flow during the radiation. They found intriguing results.

The authors found high genetic diversity within each population, and that a lot of this diversity was shared among populations, particularly between the ground finches (of which there are currently thought to be 6 species) and tree finches (currently considered 5 species). Interestingly, the authors found that there were no fixed differences between the species in each group.

One species, G. difficilis, was found to be polyphyletic, meaning a phylogenetic tree based on all autosomal sites showed three distinct groups for this species (as opposed to just one monophyletic group)—one group on the islands of Pinta, Santiago, and Fernandina, one group on Wolf and Darwin, and one on the island of Genovesa. This suggests that there may be three species, which actually matches the former taxonomy of the group based on morphology.

Another interesting finding, which helps to explain why there is so much shared genetics, was that they found evidence of extensive gene flow throughout the radiation, from early on in the groups diversification up until the present. In other words, even as speciation (apparently) was happening, hybridization and admixture between populations continued to mix up genes between populations.

However, some would argue that these data, instead of suggesting an increase in the number of species in the group, actually represent fewer species. Due to extensive gene flow, many of these taxa are not species based on biological species concept, and because there is extensive non-monophyly they aren’t species based on the phylogenetic species concept either.

Some biologists (e.g. see McKay and Zink 2014) contend that, instead, these differences in many species or sets of species of Darwin’s finches are actually more of ecomorphs than actual species. These distinct ecomorphs might be shaped by natural selection over short timescales, but then as selective pressures begin to change, the ecomorphs also change such that there is a continual waxing and waning of phenotypes, such as beak size for example, in response to changing environments through time.

However, the number of extant species resulting from this radiation is far from agreed upon.

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