Solutions to additional exercises
Genome Evolution
Additional Exercise: WGDs in Populus trichocarpa
- The same basic steps are necessary to perform this analysis as in the tutorial itself
- Though the interpretation of the results is slightly more difficult
- Interpretation of the skyline plot
- Contrary to the skyline plot in the tutorial poplar-grapevine plots reveal several times 2:1, 3-4:2, 5-6:3 ratios of segments. This already is a strong indication that there was a genome doubling.
- The WGDotplot here is slightly more difficult to interpret
- For several Vitis segments there are up to 6 poplar segments and for a poplar segment there are up to 3 Vitis segments
- The Ks value shows that for each vitis segment only 2 of the 6 segments have a recent Ks (most recent Ks in the plot is due to the speciation)
- For each poplar region there is only a single Vitis region with the most recent Ks
- This means there was in fact a poplar-specific genome doubling
- Everything else can be explained by the genome triplication that happened before the speciation. Check out the advanced tutorial for more examples like this.
