Pecking at the genome

By | Science & Technology
Close up of the large ground finch (Geospiza magnirostris), Daphne Major Island. Credit@K. T.Grant

Researchers in Sweden and the US have revealed an interesting amount of interbreeding between Charles Darwin’s finch species through whole-genome sequencing. Published in the journal Nature in time for Darwin’s 206th birthday, the study also signposts one particular gene responsible for the wide variation in beak shape.

In 1831, Charles Darwin set sail from England on a groundbreaking five-year voyage with the aim of understanding the factors that shape the diversity of life. The trip eventually landed Darwin in the Galapagos archipelago off Ecuador where he noticed that the species were similar from island to island yet perfectly adapted to their own environment. Most notable were the finches, often referred to as ‘Darwin’s finches’. He concluded that competition for survival causes the elimination of many individuals and that the characteristics of the surviving individuals are passed onto future generations. Darwin’s ‘The Origin of Species’ was a triumph. Generally, scientists accepted the concept where species had unfixed form and were not created separately. However, Darwin’s theory required a satisfactory explanation of the scientific basis for evolution.

Darwin’s finches are the textbook example of adaptive radiation where a single ancestor diversifies into different species. This is caused by directional selection – a form of natural selection that causes a directed change in a character. This type of selection is thought to be relatively common, especially in changeable environments. The classic example is selection on bill size in Darwin’s finches. The Medium Ground Finch, Geospiza fortis, which eats seeds, lives on one of the small Galapagos islands and has been studied extensively. During 1977 (a drought year), there was a very strong directional selection for large birds with large bills. This is because the average sizes of the seeds increased as drought-resistant plants typically have bigger seeds. Consequently, there was a large increase in bill size in the next generation, proving the trait to be heritable. This directional selection changes from year to year, tracking climate changes.

This study, led by Professor Leif Andersson at Uppsala University, Sweden, solidifies and expands on Darwin’s work by investigating the molecular basis of his conclusions, confirming the two century-old suspicions. Originally, Darwin grouped the finches by their morphological characteristics. This time, researchers used next-generation sequencing techniques to compare whole-genome data for all 15 of Darwin’s species. Overall, the two approaches mostly agreed, however Andersson also found a few surprises in the finch family tree. For example Geospiza difficilis may look similar however genomic data has shown they actually comprise of three different species spread across six islands.

Additionally, the team noticed extensive mixing of genes between different species. In other words, a hybridisation of species throughout this radiation contributed to the evolution of these birds. The balance between gene flow and fluctuating natural selection is likely to maintain genetic variability for individual traits, because different genes are favoured at different times.

The most distinctive characteristic between the finches is their beak morphology. By scanning entire genomes, the team was able to identify 15 candidate regions of the genome that are similar between birds with similarly shaped beaks. The most important gene in the evolution of beaks was determined to be ALX1, which codes for a transcription factor that regulates the expression of other genes. Interestingly, deactivation of this gene in humans has been shown to cause facial deformities.

Close up of the large ground finch (Geospiza magnirostris), Daphne Major Island. Credit@P. R.Grant

Close up of the large ground finch (Geospiza magnirostris), Daphne Major Island. Credit@P. R.Grant

By classifying finches as either blunt-beaked or pointy-beaked, the gene showed two distinct variants that dovetailed closely towards each beak shape, although, Geospiza fortis displayed a mixture of the two variants. Prof Andersson explained, “One is associated with pointed beaks – that is the ancestral form. Then there is a variant associated with the blunt beaks. That’s the derived form. The blunt beak version is a genetic innovation that occurred on the islands.”

Whether ALX1 drove the adaptive radiation of Darwin’s finches is unclear. The beaks differ in many other parameters, suggesting a more challenging picture involving other genes. Consequently, functional genomic studies are needed to determine ALX1’s precise role.

How might knowing this information in 1831-36 have shaped Darwin’s theory of evolution and influenced evolutionary theory today?

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