Bisulfite Sequencing Reveals the Evolution of a Popular Songbird’s Memory and Learning

The genome and methylome of a popular songbird, Parus major, or more commonly called the great tit, has just been revealed. Researchers have long awaited this data and can now use these findings to learn more about how one the field’s favorite songbirds has adapted to the changing world. Using bisulfite conversion followed by whole-genome bisulfite sequencing, the results indicate that the chemical marks above the DNA sequence that influence gene expression – known as epigenetic modifications – play an important role in the evolution of the great tit’s memory and learning. A research team of international scientists, led by the Netherlands Institute of Ecology (NIOO-KNAW) and Wageningen University, published their study in Nature Communications.

Veronika Laine and Kees van Oers from the Netherlands Institute of Ecology explained, “People in our field have been waiting for this for decades.” The reference genome of the well-known great tit is “a powerful toolbox that all ecologists and evolutionary biologists should know about.” This bird has been an invaluable model organism in ecology as well as evolutionary biology for decades.

The genetic code of the assembled reference genome came from a single Dutch bird. Now that they have sequenced its DNA, scientists can unveil the genetic underpinnings of phenotypic evolution. Novel information that can be gained from this recent accomplishment will be vital to understanding the adaptations wild species take on in response to environmental changes.

Along with the genome, the group of researchers also sequenced the methylome. The methylome is related to the field of epigenetics, which offers a view of methylated genes. The most common epigenetic modification is known as DNA methylation, defined as the addition of a methyl group to DNA via DNA methyltransferases. DNA methylation modifies the function of the genes and typically reduces gene expression.

In order to determine the methylome of the great tit, the researchers first had to carry out bisulfite conversion of its DNA. This chemical process involves converting unmethylated cytosine residues to uracil, leaving methylated cytosines (5-methylcytosine) unaffected. After bisulfite conversion, PCR amplification or massively parallel sequencing methods will recognize uracil as thymine and 5-methylcytosine (5-mC) as cytosine. This allows researchers to discriminate between which bases are methylated and which are not. In the field of epigenetics, bisulfite conversion is one of the most common methods for gene-specific DNA methylation analysis.

Overall, the researchers sequenced the whole genomes of an additional 29 great tits from various locations in Europe. Using whole-genome bisulfite sequencing, they were able to identify gene regions that were targeted for selection during the bird’s recent changes. According to the data, these particular regions contain a significant amount of genes associated with cognition and learning.

“The great tit has evolved to be smart,” Van Oers said. “Very smart.” This bird is not average –it sits at the top 3% smartest birds in regard to learning new behavior. It’s an ideal model for studying the evolution and progression of memory, learning, and other cognitive processes.

The research on cognitive processes has shown that there are conserved patterns of methylation in these regions which are also present in humans and other mammals. It suggests a correlation between epigenetic modifications like methylation and the rate of molecular evolution. Essentially, the more the genome is methylated, the more evolved the creature is, according to this association.

Even after 60 years, the great tit continues to be an incredibly useful and valuable model organism to several research fields. Now, with information about the fascinating bird’s genome and methylome, scientists can expand even further on their knowledge of memory and learning and the ways animals adapt to their changing surroundings.

Source: Laine, V.N. et al. (2016). Evolutionary signals of selection on cognition from the great tit genome and methylome. Nature Communications, 7:10474.

Reference: Netherlands Institute of Ecology. Clever songbird’s genome may hold key to evolution of learning. 25 Jan 2016. Web.