Happy New Year and a New Direction

Happy new year everyone !

Over the last three years, our blog focused on algorithms to analyze next- generation sequencing data. Most of the kinks on that front have been ironed out, whereas with availability of so many assembled genomes, it has become possible to ask interesting questions about genome evolution like never before.

So, starting from this year, we will change direction to make sense of the biological contents of eukaryotic genomes. Are there any patterns in genome evolution? How are those patterns related to the evolution of phenotypes? We have been doing extensive reading on such topics and posted many related papers in our ‘evolution and ncRNA’ blog. Starting from this year, we will continue to work more actively on these topics.

Here is a great paper to start with (h/t: @dangraur) -

Since the late 1990s, the characterization of complete DNA sequences for a large and taxonomically diverse set of species has continued to gain in speed and accuracy. Sequence analyses have indicated a strikingly baroque structure for most eukaryotic genomes, with multiple repeats of DNA sequences and with very little of the DNA specifying proteins. Much of the DNA in these genomes has no known function. These results have generated strong interest in the factors that govern the evolution of genome architecture. While adaptationist just so stories have been offered (as typically occurs in every area of biology), recent theoretical analyses based on mathematical population genetics strongly suggest that non-adaptive processes dominate genome architecture evolution. This article critically synthesizes and develops these arguments, explicating a core argument along with several variants. It provides a critical assessment of the evidence that supports these arguments premises. It also analyses adaptationist responses to these arguments and notes potential problems with the core argument. These theoretical analyses continue the molecular reinterpretation of evolution initiated by the neutral theory in 1968. The article ends by noting that some of these arguments can also be extended to evolution at higher levels of organization which raises questions about adaptationism in general. This remains a puzzle because there is probably little reason to doubt that many organismic features are genuine adaptations.