Bungo Akiyoshi

Before he passed away in 2021, Tom Cavalier-Smith had drafted parts of his autobiography. It's now 'published' because Gáspár Jékely put a lot of effort in! Please enjoy and share: doi.org/10.5281/zeno...

(BTW thanks Jalview @jalview.bsky.social)

mnmG/gidA (tRNA modification/maturation)

FUM1/fumC (Krebs cycle)

From Figshare: figshare.com/articles/dat...

I am learning a lot from this debate about the last eukaryotic common ancestor. It's thought-provoking to have competing hypotheses and perspectives argued out there in the open.

Here, the two arguments are internally consistent, yet different conclusions... so where's the wrong assumption?

Multiple sequence alignment of SDHA (Complex II subunit/assembly factor) from eukaryotes and bacteria

And to repeat, I personally do not feel it is appropriate to use bacterial-origin proteins to determine the eukaryotic root. If you look at multiple sequence alignments of proteins used in Williamson 2025, the proteins look too conserved (while archaea proteins do not show that level of similarity)

What I have been arguing is that without knowing the root position, one cannot conclude that Euglenozoa (or any group) are monophyletic. You make an assumption that the root is not within Euglenozoa when you say Euglenozoa are monophyletic.

Trypanosome histone variants H3.V and H4.V promote nucleosome plasticity in repressed chromatin pubmed.ncbi.nlm.nih.gov/41709455/

If I claimed this liquid-to-solid phase transition assay on a pure protein in vitro predicts the same transition to happen in cells, what counterarguments would you raise?

Would the same counterarguments apply to a liquid-to-liquid phase transition assay on the same pure protein in vitro?

BTW when I talked to a cell biologist this week and explained that bacterial-origin proteins were used to determine the root of the eukaryotic tree of life, the person was surprised by that approach. So it's not just me who has issues with this approach.

Hey Bungo. I don't know if you figure it out but look at this one.
From this paper: shorturl.at/Og2tn

They identify this blue light receptor only in one the posterior flagelum!

That's cool! Thanks for the information. I have not figured out anything on this

My main problem is the use of bacterial proteins that are (too well) conserved between eukaryotes and bacteria, when one knows that archaeal proteins cannot be used because they are too divergent from eukaryotic proteins. I do not think using bacterial proteins is appropriate to determine the root

I agree that euglenozoans are similar to each other, but I am saying that it does not necessarily mean that they are monophyletic due to the uncertainty in the root position.

I would argue the same from my side. Is it fair to dismiss a claim from a cell biologist whose group has shown that kinetoplastid kinetochores are entirely different?

Thanks again for the discussion

is also subjective because you make assumptions. That is the message I wanted to convey to the bioinformaticians and also the cell biology community who does not even know that the root position remains controversial. Let's see if the root position you proposed remains stable for the next decade

No, because again I am doubting the approach of using bacterial-origin proteins to solve the root of eTOL. I do not think we would ever reach any agreement because our approaches are totally different. I understand that my approach is subjective but I am saying that your (bioinformaticians) approach

Sorry I was not clear by the word evolutionary trajectory. What I meant is selection pressure (not sure if this is clear either though). How do you know that the rate of protein evolution on bacterial-origin proteins is not skewed in some lineages? Am I misunderstanding something?

What I meant is that if you know that one cannot reliably use archeal-origin proteins (because they are too divergent), how can you trust trees made by bacterial-origin proteins?

Closing date is 19th Feb so why not go for it to enjoy the rain in London!

I understand that using bacterial-origin genes clearly is clearly less prone to LBA. However, I am doubting the approach itself as I detailed in the paper.

Our views are totally different. I think my approach is more valid, and you think your approach is better.

A critical issue I have with those phylogenetic papers is that they all say their root is fully supported by their statistical analysis, yet reaching different conclusions. What can I trust?

I repeat what I replied to Max and stop. In case case, thanks for your response.

I wrote a similar thing in my manuscript but was asked to remove by one of the referees

"As a cell biologist who has worked on molecular mechanism of chromosome segregation for > 20 years, this is the possibility I feel most plausible given the uncertainty in root position".

I am fully aware of that. Yet, I do not consider it problematic because (with respect) I do not feel that the current protein-sequence-based phylogenetic approaches can solve the root position. In my paper, I wrote my reasonings including my criticism on your Williamson 2025 Nature paper.

Yes. But I am challenging that

Our views are totally different. I think my approach is more valid, and you think your approach is better.

A critical issue I have with those phylogenetic papers is that they all say their root is fully supported by their statistical analysis, yet reaching different conclusions. What can I trust?

I view this as an example showing the detection limit problem of current bioinformatics approach. Plasmodium case is another