Photosynthetic and Atmospheric Evolution
Questions re Howe's paper
1. L.J. Rothschild
When the components of a cell arise according to the "shopping bag model", at
what point do you no longer have the original organism?
That’s a good question, and I don’t know where you draw the line in that. What
I’m trying to say is that we shouldn’t think of the origin of a plastid as some event that
happens there and then, but as a prolonged process.
2. M. van der Giezen
The origin of the primary plastid may have been a prolonged experiment but was
very likely a one-off event and the subsequent loss of features happened over a long
time giving rise to the different lineages. That's why we have different plastid lineages
and not because we had different symbioses over time. The tertiary plastid is not for
nothing called tertiary.
The origins of tertiary plastids or even secondary plastids may indeed be different
from primary plastids, but that’s an assumption that we need to be aware we’re
making. We should be looking for evidence about that primary plastid origin –
whether it’s a single event or a series of events. The difficulty is that we’re looking at
something that happened a very long time ago, and it may be that all the other
phylogenetic artefacts make it impossible to answer that question in a rigorous way.
3. J. de las Rivas
Recently we have investigated the sequences of some fully conserved proteins of
Photosystem II. In particular, studying the cytochrome b-559 protein and its two
genes/proteins (psbE&F/PsbE&F) we discovered that PsbE is very much conserved
along evolution from higher plants (like spinach or Arabidopsis) to cyanobacteria
including Gloeobacter, but in the case of dinoflagellata (Heterocapsa triquetra,
Amphidium carterae, Amphidium operculatum) the sequence of PsbE ( subunit of
cytochrome b-559) is much more different, both from plants or cyanobacteria. Do you
think we still have to find some cyanobacteria that are ancestral to all these
organisms? What is your opinion about the origin or explanation of this kind of strong
difference for dinoflagellata?
I guess my opinion is don’t meddle with dinoflagellates unless you can avoid it!
They are strange organisms that do things differently from everything else, as
exemplified by this chloroplast genome organization. It’s certainly true that you find
very high substitution rates in dinoflagellate genes, so it may be that what you’re
seeing is a consequence of that.
4. N.H. Sleep
I would expect organisms that lost its photosynthetic plasmid to do poorly because
they are no longer primary producers. I realise that some organisms like Indian pipe
or ghost redwood do continue to function like heterotrophs.
Yes – so there’s an extremely strong evolutionary pressure to acquire a new one as
quickly as you can. If you have an organism that has lost its photosynthetic capability
it may well be in trouble. There are examples of other organisms that have lost their
photosynthetic capability, and they survive – non-photosynthetic mutants of Euglena,
for example. It’s not immediate death, but you need to do something about it pretty
soon!
5. J. Davies
In your shopping bag model everything you put in there has been very carefully
selected and in the course of that selection you have rejected many items on the basis
of price, or whatever. So it is not random.
Yes, I suppose the parallel to that would be that, of the genes that had accumulated
in the nucleus prior to the establishment of the latest stable endosymbiont, only some
would encode proteins that would assemble effectively with proteins present within
the symbiont. So there is a need for some kind of selection to make sure those genes
are tied in with the needs of the endosymbiont. I would argue that’s an even better
extension of the shopping bag model. It’s a good point.
6. P.G. Falkowski
At present we don't have a complete nuclear sequence for any dinoflagellate. What
is the evidence that non-photosynthetic dinoflagellates acquired plastids and then lost
them, or never had them at all? It makes a big difference to the way we account for
the phylogeny of secondary and tertiary plastids.
That’s a good question, but I’m not sure it necessarily affects the model I’m
proposing here. There are data that indicate in some non-photosynthetic
dinoflagellates the presence of sequences that are apparently of photosynthetic origin.
(References to this have been included in the revised version of the manuscript.)
7. JF Allen
This word "proof" - When you ask "Can we prove a monophyletic origin of
plastids?" you are using "prove" to mean "establish with certainty the truth of …"
This form of "prove" has no place in the natural sciences. All we can hope to do is
what William of Occam would urge us to do, which is to find the most economical
explanation that sufficiently explains that which we observe.
I knew this was going to be a discussion meeting, but I didn’t know it was going to
be that sort of discussion! (The discussions of proof and refutation have been refined
in the revised version of the manuscript.)
8. DBA Epstein
Is there a problem of methodology in the phylogenetic reconstruction used by
some workers? Phylogenetic trees are often provided without any indication of the
extent of possible errors. Related to this, are nucleotide sequences a reasonable basis
for inference on events around 1 billion years ago? Should one rather use protein
sequence structure, or even protein shape as something that changes more slowly than
nucleotide sequence.
In answer to the first question, people certainly do try to put some kinds of estimate
of statistical reliability on the trees that they construct. Now some of those methods
may or may not be reliable. A very popular method is bootstrapping. The danger is
that if you have long branch attraction you can get trees that are completely robust
under that statistical analysis even though they are in error. In terms of your second
point, I would agree with you completely that phylogenetic analysis, particularly for
these ancient divergences, needs to be understood in conjunction with information on
protein structure, protein function, what are the regions of particular molecules that
are interacting with others – and therefore which sites are free to vary and which
aren’t. Systematic biases can be very dangerous indeed in phylogenetic
reconstruction.