I suppose I should reduce my salt intake. Still, I take your point. One thing that all these phylogenies seem to share is that they are all different. And generally the authors draw conclusions that involve implicit assumptions. For example, do species evolve in isolation? Probably not. Are chloroplasts immune to the effects of natural selection? I don’t know.
I do think it would be interesting to see a map of chloroplast genotypes, ignoring (for the moment) the species in which they are found. Would there be a pattern? Would some genotypes be found more commonly in damp woodlands, others in the prairies, and still others in deserts?
The same principle might apply to DNA snippets. The bits studied might not have selective value, but they could be linked to other bits that are useful to the plants in some conditions.
Nevertheless, the various studies raise some interesting possibilities. I recently learned a couple of things that surprised me. For one, Fragaria (strawberries) has been merged with Potentilla. I must have been asleep that year. And according to one DNA-phylogenetic study, Rosa is closer to Potentilla/Fragaria than it is to Rubus. This is striking because Burbank raised hybrids from Raspberry x Strawberry, which are (supposedly) more remote than Rosa and Fragaria.
http://bulbnrose.x10.mx/Heredity/Burbank/Burbank_raspXstraw.html
Does this mean we could breed yellow roses from yellow cinquefoils? I wouldn’t bet, but you never know. The flowers of Potentilla reptans contain β-Carotene, 5,6-monoepoxyde of α-carotene, 5,6:5′,6′-diepoxide of α-carotene, 5,6:5′,6′-diepoxide β-carotene, cryptoxanthin, epoxide of cryptoxanthin, mutatochrome, lutein, trans-epoxide of lutein, cis-epoxide of lutein, flavoxanthin, auroxanthin.
Oh, and one more thing. I had never heard of Dalibarda, an herbaceous plant with heart-shaped leaves (like a violet), and both chasmogamous and cleistogamous flowers (like a violet). Now I learn that it nests within Rubus (DNA-wise), and has been taxonomically reunited with that genus.