Peripheral structures in unlabelled trees and the accumulation of subgenomes in the evolution of polyploids
This repo contains reference codes of phylogenetic analysis of Saccharum officinarum as described in the following paper:
Peripheral structures in unlabelled trees and the accumulation of subgenomes in the evolution of polyploids
Pouryaha, F., Sankoff, D.
Submitted to the Journal of Theoretical Biology, 2021.
Many angiosperms have undergone some series of polyploidization events during their evolution. In these genomes, it may be relatively easy to recognize all ξ sets of n homeologous chromosomes, but it is much harder, if not impossible, to partition these chromosomes into n subgenomes, each representing one distinct genomic component of ξ chromosomes making up the original polyploid. We suggest that despite of lacking a consistent 1-1 correspondence between the chromosomes in different sets, the topological structure of the trees may display sufficient resemblance so that a higher level consensus could be revealing of evolutionary history. This would be especially true of the peripheral structures of the tree, likely representing events that occurred more recently and have thus been less obscured by subsequent evolutionary processes. In this paper, we present a statistical test to assess whether the subgenomes in a polyploid could have been added one at a time. The null hypothesis is that the accumulation of chromosomes follows a stochastic process in which transition from one generation to the next is through randomly choosing an edge, and then subdividing this edge in order to link the new internal vertex to a new external vertex.
Autooctoploid sugarcane genome elucidates sucrose accumulation and female restitution
Ming, R. \ et al. In press 2021.