When did Mitochondria Evolve? - Comments

[Ygggdrasil]

Ygggdrasil submitted a new PF Insights post

When did Mitochondria Evolve?

Continue reading the Original PF Insights Post.

 

[jim mcnamara]

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.

 

[jim mcnamara]

Very well done write up. It triggered some some thoughts related to chloroplast evolution. Thanks for a nice job.

 

[Greg Bernhardt]

Great as always!

 

[Torbjorn_L]

Very useful synopsis, as the paper is on my to read pile!

Some hasty reflections:

- 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 ER and nucleus has the wrong topology to be inherited vertically as a functional unit. Rather the Lokiarchaeota paper solves this.

- Both the Lokiarchaeota paper and the mito-late result would be consistent with the latest mitochondrion phylogeny (that I know of). Having the mitochondrion ancestor as an energy parasite could mean many infestations before the parasite was captured and defanged by increasing mutualism. [ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110685 ]

- 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!

 

[Ygggdrasil]

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.

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 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.

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

Interestingly, in the supplementary materials of the Pittis and Gabaldón paper, they claim that the group of bacterial-origin genes they identified to be putatively involved in the endomembrane system are not present in the Lokiarchaeota sample.

- 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!

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.

 

[Ygggdrasil]

UPDATE: William Martin and co-authors have published a (non-peer reviewed) critique of the Pittis and Gabaldón study. They take issue with the use of stem-length (sl) as a measure of evolutionary age and with some of the methods used to analyze the data in the original publication:

In 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.

Martin et al. 2016. Late mitochondrial origin is pure artefact. bioRxiv doi:10.1101/055368

The full paper is freely available at http://biorxiv.org/content/early/2016/05/25/055368

 

[Antoine199]

UPDATE: Please see the response to the critique.
http://treevolution.blogspot.ca/2016/05/response-to-late-mitochondrial-origin.html