Wednesday, November 9, 2016

Heterogeneous genome differentiation : crow hybrid zones

Our paper about the analysis (mostly characterization, with some new ideas) of the genome wide differentiation landscape in more than 100 crow genomes is now available to read. With a title that reads "Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex" we hopefully portray the appropriate message. The message would be that it is rather easy for a well managed and well funded lab to choose a study system and build it up to a level of a model system rather quickly. The uniqueness of the study is the presence of replicate hybrid zones, being able to contrast the phenotypes at different evolutionary distances and try and disentangle how selection acts across the genome.

We say "..parallelism by pathway rather than by repeated single-gene effects." I like this part in that it suggests multiple genes that can lead to the same phenotype. However, pinning down the actual genes and the causative variants is easier said than done. Systems that are easier to manipulate with much more historical context are still not resolved to this resolution. This is not to say that this work is not needed. It definitely is needed before we go to the next step. Numerous bird species have come to a stage where these resources have been developed. Integrating these data into a theoretical framework that spans multiple study systems will probably still take time.

The main result of the paper is basically figure 2, which tries to subtract out the background signals and find signatures that are unique to each hybrid zone. Similar attempts are underway in various other species with slightly more rigorous models. Some incorporate recombination rate maps, others use sequence conservation across species. A resolution of how common selective sweeps (hard, soft, partial etc.) are in natural populations as well as the methodology to detect them will probably still have to play out as functional validation methods are developed.

No comments: