If I only have one single individual in one of the species analysed, is the analysis reliable. How do we interpret the results? Should we put each three figures generated from the analysis into publication or just select the base partition?
Generally spoken comparisons of distances within species to distances among species are more reliable if we have good proxies of intra- versus interspecific variability, thats clear.
If now among many compared species a single species is represented by only a single specimen I would nevertheless calculate the values. (By the way a higher number of representatives, if derived from a single Population often hide the fact, that the Proxy for intraspecific variability is not much better than in datasets containing a single specimen).
I would say more important is the way we discuss such data.
If you have a dataset that does not give a good estimate for intraspecific Variation, this should be clearly stated in your discussion of your data. then as a reviewer i would have no Problems with analyses that reflect our current knowledge.