Auto vs allo ploidy

[bshahid5]

Hello!
I am trying to infer whether a tetraploid plant species (Dianthus gratianopolitanus) is an allopolyploid or autopolyploid. I suspect it to be an allopolyploid with an AAAB structure (I have confirmed AAAB structure from a few samples using genomescope and smudgeplot already).
Reading the literature, it looks like okra and cotton show something similar (allopolyploids having AAAB genomic structure). In your paper, GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes, you show genomescope profile of Gossypium barbadense which shows aabb>aaab (are these percentages of nucleotide positions?)

However, the smudgeplot in the supplementary shows higher proportion for AAAB (0.1) compared to AABB (0.04), and incorrectly identified as a diploid which you discuss could be because of how divergent the genomic copies are.

I was hoping you could help me understand this result and to whether you would expect smudgeplot result to show higher count for AAAB compared to AABB even though that's not what genomescope shows and from what I know, G.barbadense is also an allopolyploid. Does this suggest that the AAAB structure could indeed also indicate allopolyploidy and is there a way to further confirm this theory?

Thank you so much for this wonderful tool and your help!