Question

2- Prüfer et al. (2014) chose to build a phylogenetic tree connecting Denisovans to Neanderthals and modern humans that was based solely on autosomal transversion substitutions. In other words, Prüfer et al. simply ignored (did not count) any sequence locations that had experienced a transition substitution, and they also did not count both sex chromosomes. Why would they make those choices? What would be the scientific costs and benefits of those choices?

Prüfer, K. et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43-49.

Answer 1

• The genomes of common ancestor which leads to Denisovans , Neanderdhals are shorter compared to the present day humans.
• This shows that the genomes of Denisovans and Neanderdhals stopped accumulating the substitutions at the time of death of the the individual. That is why they are shorter than present day humans .
• More over by analysing the present human genome with nearest ancestor shows that there are only minor differences in the substitutions between ancestor and present day human. So these substitutions can be ignored.
• So, Prufer et al preffered present day genomes of higher quality and so the cost is reduced by one third and also error rates are reduced drasitically.