Thursday, November 17, 2016

Stable polypoidy in yeast identified through experimental evolution

The paper we discussed today in the journal club is a topic that has always been very fascinating. Polyploidy, especially speciation driven by polyploidy is thought to be very common among plants. Janaki Ammal, "attributes the higher rate of plant speciation in the northeast Himalayas compared to the northwest to polyploidy" in her paper : The effect of the Himalayan uplift on the genetic composition of the flora of Asia. Infact, a lot of work done by her revolves around polyploidy. Some of this work is fascinating and seems relevant even today. One could continue her research program today and still be very current.

Coming back to the paper, it is yeast not plants. It makes it easier to study due to the ease of manipulation. Title of the paper is "Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast". After constructing the strains, experimental evolution was conducted for 1000 generations to evolve the required strains. All that is needed for figure 1 and 7 is flow cytometry. Figure 3 and 5 are both relative fitness assay's and seem doable but need a lot of work. However, figure 2 and 4 need a array platform and might be out of reach.

The fact that they are able to pin down the the Sch9 gene and the TORC pathway takes the paper to the next level. Although it is not clear what the mechanism is or how general and widespread this pathway can be in stabilizing polyploidy. It would of course be interesting to see if the natural polyplod isolates from the evolution canyon show changes in this very pathway.

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.