I haven't looked too in depth into chloroplast evolution or thykaloid evolution in cyanobacteria, but those are good thoughts. Chloroplasts are believed to have evolved after mitochondria through endosymbiosis with a fully eukaryotic host containing nucleus, endomembrane system and mitochondria (here's a nice review article on the evolution of chloroplasts). However, perhaps the beginnings of an endomembrane system evolved in an organism like cyanobacteria and got transfered to the eukaryotic ancestor at some point.I'm not current in this field. A priori, an understanding of chloroplast development should help verify the endomembrane when question. Do you have any links on this? Chloroplasts have membranes within membranes - e.g., thylakoid membrane. Cyanobacteria are candidates for a possible endosymbiotic source for chloroplast development.
Yes, the hypothesis argued by the Lane paper is controversial. Here's one criticism of the hypothesis published recently in the Proceedings of the National Academy of Sciences: http://www.pnas.org/content/112/33/10278.abstract- I am not surprised after the Lokiarchaeota phylum result. Moreover the usual comparison between prokaryote and eukaryote energy efficiency (such as Lane's) is problematic. Comparing apples with apples prokaryotes can sustain about as large protein turnover (so large genomes) as eukaryotes. [ http://book.bionumbers.org/what-is-the-power-consumption-of-a-cell/ ] And I think there is a paper that directly comes to the same conclusion. [A lost reference as I write this in haste. :-/] So mito-late would presumably be viable.
The tree criticism is somewhat valid given that the paper is trying to understand horizontal gene transfer, something that tree models are not designed to handle. It's possible that imposing a tree model on a more complicated evolutionary process could cause some of the molecular clock estimates to be wrong.- The "controversy" reference is peculiar in criticizing the use of trees by default since coarse history is well captured by them, including the endosymbiosis in question!
Martin et al. 2016. Late mitochondrial origin is pure artefact. bioRxiv doi:10.1101/055368In summary, sl-based conclusions about eukaryote evolution are unfounded, resting upon fatal
flaws in i) over-fitting of the wrong distribution model, ii) analyses of non-independent data,
and iii) implicit, untested, and untrue molecular clock assumptions.