Joint allele frequency spectrum is allele frequency distribution calculated between two\three populations. Imagine a 2D plot, where on x axis is AFS of population 1 and on y axis is AFS in population 2. For example, you can plot derived allele counts in Yoruba versus Central European population. Let's say, you count allele A x times in Yoruba and y times in Central Europe, then you plot it on 2D space. For three populations it will be a 3D plot. Upscaling this to a higher number of populations is computationally very hard.
Joint AFS is informative about migrations and other parameters, because changes in jAFS will reflect changes in demography.
Take a look at this paper by Gutenkunst et al http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000695