From what I understood, allele frequency spectrum is everything that concerns the frequency of all of the alleles studied in a population. It can be estimated with Tajima's D, theta, etc.
But how is it different from the joint allele frequency spectrum?
Cool! That's great! But if I read the axis on the graph, it's from 0 to 20 which makes 21 comparisons.
Where is the 21th comparison coming from? Also, is JAFS only on chromosomes or it can be on SNPs?
In addition if you have 2 populations, it's actually a 3D graphs (the elevation is the colour). Also, usually, the colour is the number of SNPs between two chromosomes. Can it be something else?
My explanation is very simplified, I just made it to be intuitive. Furthermore, I guess these numbers may be log-transformed for plotting, and I don't remember exactly what they did for these figures. AFS is estimated from allele counts, i.e. how many times you see a SNP in a population. 20 chromosomes means there were 20 haplotypes, which can mean, for example, 10 imaginary individuals with a pair of chromosomes in each. I suggest reading this paper, it goes into details about allele counts, AFS and related concepts https://www.nature.com/articles/nrg4005