2 posts were merged into an existing topic: Still more Comments on Ewert’s Dependency Graph
It is characteristic of the eukaryotic HGT literature that the mechanism of transfer is bracketed as “unknown” or “an area for further research,” usually in the Discussion section of the paper.
Support for the HGT hypothesis in question therefore rests entirely on the phylogenetic anomaly.
That isn’t quite right. There are other signals and observations than merely the phylogenic anomaly.
If I started listing all the fields that can be described in this way, I’d get nothing else done for a couple of days.
That is a blatant falsehood and it’s really disappointing to see.
I forget: has Paul Nelson gone on record as denying that processed pseudogenes exist?
???
The “HGT hypothesis” flows from the phylogenetic anomaly. Research about mechanisms thereafter draw upon what we know about HGT in various systems.
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“Could it be that eukaryote LGT does not really exist to any significant extent in nature, but is an artefact produced by genome analysis pipelines?”
https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201700115
I just skimmed that paper and found unsurprisingly that it doesn’t support your false statement and isn’t about mechanisms of LGT, which was a few hours ago the topic of the thread. It’s definitely interesting in its own right, and so it’s a shame that it has become another quotemined piece of real scholarship.
So, to reiterate: the quote below is a careless falsehood. Disappointing, and tediously so.
If there is no further interest on your part in the topic of mechanisms of gene transfer, I’ll get back to some real work. To other participants in this thread: consider looking up “Occam’s broom” as it gives insight, IMO, into the conversation.
Thanks for posting the examples of germline HGT. Had not seen them yet. Gonads are immunologically privileged. Does that make HGT more or less likely?
Read, don’t skim. From p. 8, my emphasis:
“Should LGT be the new default explanation for ‘unexpected branches’ in eukaryotic phylogenetic trees? We can easily remedy the ‘unexpected branch problem’ with measures less dire than LGT, for example, by assuming that occasional phylogeny artefacts are a normal and unavoidable component of phylogenetic reconstruction. Part of the problem is that trees with unexpected branches can readily be published as evidence for eukaryote LGT in many journals […]”
Phylogenetic anomaly, no evidence of mechanism of transfer. This is directly relevant to the question in the OP of the mechanism of transfer, if one takes the time to disarticulate the logic of the LGT / HGT inference.
Human and animal cells grown in the lab can be readily transfected with plasmids using simple agents such as calcium phosphate.
Eukaryotic organisms are known to be capable of taking in “naked” foregin DNA found in the environment, and plasmid transfers between eukaryotic cells such as yeast have been documented.
@pnelson he is saying something different. He is saying that phylogenetic anomalies can be explained by either reconstruction errors or HGT, so we shouldn’t assuming HGT without ensuring it wasn’t a reconstruction error.
This doesn’t seem to give much support to your point, @glipsnort and @Dan_Eastwood have already made the point already.
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With the use of phylogenetics and comparative genomics, we also know that HGT is very rare in most complex animals.
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Which makes the title of that article extermely misleading:
That term “hallmark” doesn’t sound right at all.
Indeed. I count 3 HGT events in the human lineage since the primate common ancestor. I would call that rare. In the other groups we are looking at less than 200 events over very long time scales which is a drop in the bucket compared to a 10,000 to 20,000 gene count with some turnover.
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And just 1 in our evolution from common ancestry with the Great Apes. Rare indeed. It might even be a reconstruction error…
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That doesn’t back up your false statement and you should be able to see why. I have no further comment on that.
I’m sure it hinders HGT all things considered, but the thread was about eukaryotes, which include vast numbers of lineages to which “gonad” and “immunologically privileged” don’t apply. If the topic of this thread had been “HGT in mammals” I wouldn’t have bothered to respond.
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Maybe we are reading @pnelson wrong here. I admit I am/was anticipating that @pnelson’s argument would look something like the quote here. In citing Martin’s paper, it would seem as if @pnelson is actually raising questions about the authenticity of supposed phylogenetic anomaly. This is good practice - if the anomaly doesn’t exist, if it is an artifact of the technology and analysis, then there is no reason for anyone to get excited about it. And certainly no reason to start talking about a lack of a mechanism (for something that isn’t real) or problems for evolutionary theory.
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Did you know mammalian and yeast cells can be transformed with Agrobacterium?