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Friday, May 18, 2018

Is lateral gene transfer (LGT) Lamarckian?

There's an interesting discussion going on about lateral gene transfer (LGT) in eukaryotes. LGT is the process by which DNA from one species invades the genome of another species. It was apparently very common among primitive bacteria several billion years ago and it's still quite common in modern bacteria.

There are many reports of LGT in eukaryotes but some of them seem to be due to contamination from bacteria rather than true LGT. Many scientists are skeptical of these reports; notably Bill Martin (Heinrich Heine Universität, Düsseldorf, Germany) who suggests that almost all of them are artifacts and lateral gene transfer in eukaryotes is extremely rare [see Lateral gene transfer in eukaryotes - where's the evidence?].

Andrew J. Roger studies deep evolution at Dalhousie University in Halifax, Nova Scotia, Canada. He has vigorously defended the existence of LGT in eukaryotes (see his comments in my earlier post).

In addition to this debate about the existence of LGT in eukaryotes, there's a discussion about whether lateral gene transfer in eukaryotes, if it exists, is a fundamentally Lamackian process. The latest exchange took place with two letters published in the May issue of Nature Ecology & Evolution.
Eukaryote lateral gene transfer is Lamarckian, William F. Martin
[doi: 10.1038/s41559-018-0521-7]

Reply to 'Eukaryote lateral gene transfer is Lamarckian,' Andrew J. Roger
[doi: 10.1038/s41559-018-0522-6]
Martin is mostly concerned about adaptationist claims of LGT in eukaryotes. He references a number of papers that make such claims; for example, Hirooka et al. (2017) claim that the green alga, Chlamydomonas eustigma, recently adapted to an acidic environment by taking up genes from bacteria or other eukaryotes. These genes are not present in related species that have not adapted to an acidic environment. Here's how Martin describes such studies.
The core of eukaryotic LGT adaptation claims is that eukaryotes lack the genetic material required to survive in particular environments and acquire the genes needed in order to access those environments from those that already live there. Lamarckian? Yes. In eukaryote LGT adaptationism, the environment is the source of natural variation, not the evolving organism itself.
I see Martin's objection as essentially an attack on naive adapatationism invoking LGT as a mechanism for adaptive change. The fact that many of those claims of LGT are probably false is only part of the problem. The other part is the adaptationist claim to justify recent and abundant LGT.

It's true that there are Lamarckian characteristics behind these (probably false) claims. However, that's probably not the best way to criticize the hyper-adaptationism that's associated with false conclusions about LGT in eukaryotes. In addition, Martin clearly goes too far when he implies that all eukaryotic LGT is Lamarckian and false.

Andrew Roger takes up the challenge implied by Martin's exaggeration. The gist of his argument can be found in the first two sentences of his letter ...
Martin argues here and elsewhere that nearly all claims of lateral gene transfer (LGT) into eukaryotic genomes are untrue, and that accompanying narratives are fundamentally 'Lamarckian.' Some eukaryotic claims have proven false, but this does not mean that most are. Although rare, gene transfers have had a profound effect on the evolution of traits in eukaryotes.
He goes on to explain the "proper" view of LGT.
Chunks of DNA are accidentally incorporated into chromosomes creating genetic variation that is neutral, deleterious or, in rare cases, beneficial. If they enhance fitness, acquired genes are likely to be fixed in the population by natural selection. Any reasonable adaptive LGT claim has a similar etiological narrative that respects modern evolutionary principles.
Here's the problem. Martin knows the proper role of LGT but that's not what he was criticizing. He was criticizing many "unreasonable" adaptive LGT claims but he went too far by implying that all claims were of this type.

The real issue here is that a great many claims of LGT in eukaryotes are probably false—I suspect that most are false. We should not let bickering over Lamarck obscure that fact. I wish Bill Martin had not raised the issue about Lamarckian evolution.
The world is not inhabited exclusively by fools and when a subject arouses intense interest and debate, as this one has, something other than semantics is usually at stake.

Stephan Jay Gould (1982)

As Stephan Jay Gould once said, when scientists squabble over semantics, there's usually something more at stake. In this case, it's the origin of basic metabolic processes. Martin is one of a group of scientists who propose that primitive eukaryotes were facultative anaerobes. They were capable of growing and reproducing in the presence of oxygen and in its absence. They acquired this capability because the primitive mitochondrial endosymbiont had all of the enzymes necessary for both types of metabolism. In some lineages, the ability to carry out anaerobic metabolism has been lost. This hypothesis is sometimes called the "hydrogen hypothesis" because an important terminal electron acceptor is protons that can be reduced to form hydrogen.

Here's how Müller at al. (2012) explain the controversy over the origin of anaerobic metabolism in eukaryotes (e.g. protists).
For the origin of anaerobic energy metabolism in protists, the question is, Were the genes present in the single eukaryote common ancestor, or do they clearly reflect multiple origins, and if the former is true, does their single origin coincide with the origin of mitochondria? This has in turn given rise to two main competing alternative hypotheses for the origin of anaerobic energy metabolism in protists: (i) the enzymes were present in the eukaryote ancestor and were inherited vertically by modern groups, or (ii) they were lacking in the eukaryote ancestor (which would then implicitly have been a strict aerobe) and were acquired in different eukaryotes groups independently via lateral gene transfers (LGTs). Those views generated very different predictions with regard to the evolutionary patterns of the underlying genes.
The authors, including Bill Martin, conclude that the enzymes were present in the early mitochondrial ancestor although they don't preclude that 1-2% of the genes could have been acquired by LGT.

Andrew Roger has proposed that many of the genes required for anaerobic metabolism were acquired by LGT after the initial symbiotic event (Hug et al., 2010).

Thus, the two participants in the exchange of letters are on opposite sides of the bigger debate on the origin of genes for anaerobic metabolism in eukaryotes. Bill Martin favors the hydrogen hypothesis and the idea that the primitive bacterium giving rise to mitochondria was a facultative anaerobe carrying the genes necessary for anaerobic metabolism. These genes have been lost in many eukaryotes but the core genes all descend from a common ancestor. Andrew Roger is on the side of those who argue that anaerobic metabolism arose independently by LGT in many eukaryotic lineages. This is why he ends his letter in Nature Ecology & Evolution with ...
So why such resistance to LGT in eukaryotes? Endosymbiotic organelle origins and endosymbiotic gene transfer have been championed as dominant mechanisms in eukaryotic gene evolution. Indeed, the widely publicized 'hydrogen hypothesis' of eukaryogenesis depends heavily on assuming a mitochondrial ancestry of 'bacterial-like' enzymes of anaerobic energy metabolism in eukaryotes. Acknowledging LGT as an important mechanism provides an alternative explanation for such patchily distributed genes in eukaryotes that do not show the hallmarks of mitochondrial or plastid origin.
Keep in mind that if Andrew Roger is correct about how laterally transferred genes are eventually fixed in a lineage, then LGT must be very common because most events will not give rise to an adaptive advantage. They will be neutral or disadvantageous. Bill Martin believes that most claims of LGT in eukaryotes are false—he's probably right about this—and that LGT must be quite rare. If Bill Martinis is correct then it's unlikely that LGT can account for all the examples of anaerobic metabolism in eukaryotes.

I'm not a big fan of either explanation for anaerobic metabolism. The idea that it's the primitive condition that has been lost in may lineages seems a bit far-fetched given the patchy distribution in eukaryotes. On the other hand, using LGT to explain this patchy distribution of fundamentally similar enzymes activities seems equally unlikely.

The various tests of these hypotheses relay on sophisticated analyses of sequences that diverged billions of years ago. Both of these men (Roger and Martin) are experts in this field but they are pushing the boundaries of the field using algorithms that are incomprehensible to the average scientist.

Photos: The first photo is of Bill Martin and me having coffee at Tim Hortons in Toronto last year. The second one is Andrew Roger and me at the "Tree of Life" meeting in Halifax in 2009.

Hug, L.A., Stechmann, A., and Roger, A.J. (2009) Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes. Molecular Biology and Evolution, 27:311-324. [doi: 10.1093/molbev/msp237]

Müller, M., Mentel, M., van Hellemond, J.J., Henze, K., Woehle, C., Gould, S.B., Yu, R.-Y., van der Giezen, M., Tielens, A.G., and Martin, W.F. (2012) Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiology and Molecular Biology Reviews, 76:444-495. [doi: 10.1128/MMBR.05024-11]


Joe Felsenstein said...

In addition to all this one could ask what "Lamarckian" means. Lamarck believed that there was an inherent complexifying force in biological evolution, in effect a directed mutational force. In addition, he believed that in trying to use, or failing to use, its structures an organism affected the inheritance of those phenotypes. If theories have these processes in them, they are truly Lamarckian. I'd say that the theories that Bill Martin and Andrew Roger are arguing about are actually not Lamarckian.

I'm quibbling about definitions. Note that this point does not actually say anything about which of them is right, or righter. Just who gets to call what Lamarckian.

David Pollock said...

Larry, I've been following this from a distance (know both the players), and found your comment (and the linked papers) that "the origin of basic metabolic processes" was the deeper issue at stake to be quite helpful. I agree with your and Joe's complaints about "Lamarckian" being thrown in (probably incorrectly) and distracting from the real issues.

AJR said...

I agree completely that Lamarck has nothing to do with this discussion and is a red herring. Please note that it was Bill Martin, not me, that suggested it had anything to do with Lamarckism. As I said in the Nature Ecology and Evolution correspondence: "What about the charge of Lamarckism? It is groundless." and then after describing the mechanism as Larry quotes above, I said: "Is this Lamarckian? No. Like other mutational mechanisms, LGT processes are not directed by their potential fitness effects. Furthermore, acquired genes are not phenotypic characters of organisms that are modified by habits of use; only the latter are relevant to Lamarck’s original ideas [10]. Some authors reinterpret Lamarckism in light of molecular genetics [11], arguing that LGT in both prokaryotes and eukaryotes constitutes a form of ‘quasi-Lamarckian’ evolution. They suggest that environments are enriched in genes ‘adaptive’ for life in that environment by virtue of the organisms that inhabit them. An organism entering this environment therefore has a higher chance (relative to another environment) to sample an ‘adaptive’ gene by LGT. However, even in this account, the outcome of LGT is still probabilistic with respect to fitness. Rather than being Lamarckian, this phenomenon is better seen as the biased availability of mutations causing directional evolution [12]."

Reference 10 is an authoritative review of Lamarck's work by Burkhardt (see Burkhardt, R. W. Lamarck, evolution, and the inheritance of acquired characters. Genetics 194, 793–805 (2013).

Reference 11 is to Koonin and Wolfe who suggested LGT can be 'quasi-Lamarckian'(Koonin, E. V. & Wolf, Y. I. Is evolution Darwinian or/and Lamarckian? Bio. Direct 4, 42 (2009)

Reference 12 is to Stoltzfus and Yampolsky, (2009) (Stoltzfus, A. & Yampolsky, L. Y. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J. Hered. 100, 637-647) who discuss directionality in evolution resulting from biased availability of mutations.

AJR said...

Larry has correctly portrayed the ultimate source of the disagreement: the origins of anaerobic metabolism in eukaryotes. Some additional references on this topic might be helpful:

Stairs, C.W., Leger, M.M. and Roger, A.J. Diversity and origins of anaerobic metabolism in mitochondria and related organelles. (2015) Philos Trans R Soc Lond B Biol Sci. 370:20140326

Leger M.M., Eme L., Stairs C.W., Roger A.J. (2018) Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115) Bioessays 40:e1700242.

Larry Moran said...

Note to readers: AJR = Andrew Roger

Larry Moran said...

It's not productive to argue about whether LGT is Lamackian or not.

Let's talk about the main problem with your proposed mechanism. In order for your explanation to work, the uptake of DNA from the environment has to be sufficiently frequent to allow an organism to acquire specific genes for anaerobic metabolism in order to invade an anaerobic environment. It has to take up and incorporate thousands of genes from a variety of different species in order to have any chance at all of randomly finding the "right" ones.

Then it has to fix those genes in the population. As you know, this is is not guaranteed even under selection. In this case, the organism has to be living in an anaerobic environment in order for selection to be effective.

If this were the mechanism of acquiring the right genes then we would expect to see all kinds of examples of LGT in every lineage. Most of them would be nearly neutral and would have been fixed by random genetic drift. As Bill Martin points out, under this scenario we would expect most eukaryotic species to have pangenomes as in bacteria.

I don't think the evidence supports the level of LGT required for your scenario to work in eukaryotes. This is why so many scientists have implied an adaptationist explanation where, somehow, the organism is able to specifically select the "right" genes to incorporate and avoid all the noise that would arise from a "proper" evolutionary explanation of LGT.

Larry Moran said...

Note to readers.

Martin and Roger have been fighting about this issue for several years. There are many papers to read.

I did not mean to imply in the comment above that Andrew Roger has never addressed this issue in print. He has. I mostly wanted to alert Sandwalk readers to the issues that are being debated.

William Martin said...

I think Larry has, as usual, gotten very much to the core of the issue. The point is that the eukaryote lateralists are basically arguing directed transfer for specific genes (for oxygen sensitive enzymes), in some of their papers transfer of a functionally connected suite of enzymes (a module). Those transfers generate what they themselves are calling adaptations (access to a new niche). They are welcome to believe what they want. But when they start saying that eukaryotes acquire genes to access new niches then they are telling students and the public that this is how evolution in eukaryotes works: acquire genes to adapt. Should we believe that?

Why is it only the traits that they study and not all traits? The simplest interpretation is that they are overinterpreting the branches in single gene phylogenetic trees. With the help of some talented students and collaborators, I have been looking at the trees for all the genes that eukaryotes harbour, and all the genes that eukaryotes share with prokaryotes. When we do that, there are no cumulative effects of eukaryote LGT to be found, while cumulative effects of LGT in prokaryotes abound. If all the LGT that the eukaryote lateralists infer from branches in single gene trees is real (as opposed to artefact), then it should be going on for other traits, too, and it should lead to cumulative effects. Neither is observed. So I point that out in an assay.

The eukaryote LGT community has become uncritical, the 17% LGT tardigrade being the case in point. They are welcome to believe what they want, but when they tell students that eukaryotes have some secret lateral genetic life that only spreads genes for one kind of trait, then I wonder whether there are simpler explanations for the same observations, like presence of the genes in the eukaryote common ancestor and differential loss. But the news value of such a normal evolutionary process is not sufficient in some circles, I suppose, so folks want to hype it up with LGT stories. Such is evolutionary biology in 2018.

If you think I am anti-LGT, I can assure you that is not the case: just go back and read Doolittle's 1999 Science paper that (over?-)popularized LGT and see whose papers and figures he was leaning on to make his case -- the Martin he was leaning on is me.

LGT in prokaryotes is real and leaves cumulative effects. Patterns that people interpret as LGT in eukaryotes can usually be interpreted by alternative means. The eukaryote lateralists are using LGT as their first line of explanation for patterns and support values in single gene trees for eukaryotic genes. I think it should be the last line of explanantion.

What is life? Life is short.

David Pollock said...

Larry, I wonder if you could shore up your argument a little bit, as it doesn't appear to me to be very strong. If eukaryotes are generally prone to find exogenous DNA slightly deleterious, your neutral frequency argument would be irrelevant. Also, I expect anaerobic environments are a gradient, and not implausible that the organisms involved in putative LGT would be living together under conditions where LGT of genes would be beneficial to the recipient. I don't agree with your assumptions about what the frequency evidence means.

Are there any unspoken biochemical arguments in your thinking?

The true meat of the argument seems to be whether it did or did not happen, based on phylogenetic evidence (which I do find comprehensible, but deferring judgment atm).

William Martin said...

When scientists see unexpected branches in phylogenetic trees the first reaction is to get excited and to interpret the branches as direct evidence for a new evolutionary process. Maybe there are simpler factors like model misspecification, paralogy, and differential loss that can explain unexpected branching patterns. I reiterate that adaptation (n.b. adaptation, read the lateralist papers) to anaerobic environments does not hold water as an evolutionary explanation when the genes involved are present in organisms the produce oxygen.

Atteia A, van Lis R, Tielens AGM, Martin WF: Anaerobic energy metabolism in unicellular photosynthetic eukaryotes. Biochim. Biophys. Acta Bioenergetics 1827:210–223 (2013).

It is fairly evident that the genes involved in anaerobic energy metabolism were present in the common ancestor of red, gree, and glacophyte alge. Most folks would date that at about 1.4 billion years ago, at least. That is outlined in this paper among others.

Martin WF, Garg S, Zimorski V: Endosymbiotic theory for eukaryote origin. Phil Trans Roy Soc Lond B 370: 20140330 (2015).

So as I see it, the onus is upon eukaryote lateralists to go the full monty, or the whole nine yards, and really place eukaryote LGT in the more general context of the mechanisms governing eukaryote evolution. What about phagocytosis, missing in many eukaryotes:

Martin WF, Tielens AGM, Mentel M, Garg SG, Gould SB: The physiology of phagocytosis in the context of mitochondrial origin. Microbiol Mol. Biol. Rev. 81:e00008-17 (2017).

Maybe the lateralists can find evidence for the lateral passing around of a module of genes for phagocytosis, too. Or maybe there is evidence for the lateral spread of genes for eukaryotic flagellae. And has anyone looked for evidence of lateral transfer of genes for having an endoplasmic reticulum. Cortical alveolea, another trait that could be spread via LGT. The list begins to grow to exciting dimensions. Absence, or reduction, in some lineages has been traditionally explained by loss. But -- nobody has carefully inspected the trees, there might be some unexpected branches in there that could be a rich research area for eukaryote LGT. Go for it, lateralists.

And while the lateralists are at it, they need in their fuller lateral eukaryotic synthesis to explain the geological timing of how genes for the anaerobic lifestyle were passed around throughout the various algal lineages --- in a manner that also accounts for each of the unexpected branching patterns that make up the foundation of their LGT theory (and the presence of five divergent copies). And then they need to explain why the genes are acquired to confer adaptation to anaerobiosis when the same genes are present in organisms that produce intracellular oxygen. Is there something about the eukaryote LGT argument that the lateralists are not telling us?

Eukaryote lateralists, I offer, need to apply their explanantory principle and get more general. Maybe meiosis was also passed around via LGT? Again, conservative wretch I am, I think that meiosis, like the handful of genes that are the backbone of pyruvate metabolism in eukaryotes, was present in the eukaryote common ancestor.

Garg S, Martin WF: Mitochondria, the cell cycle and the origin of sex via a syncytial eukaryote common ancestor. Genome Biol. Evol. 8:1950–1970 (2016).

There are so many exciting traits that could have been passed around via LGT in eukaryotes. Hair, vertebrae, eyes, nerve cells, roots, the excavate feeding groove, the ability to colonize land, flagellae. Why go to the trouble of evolutionary invention and retention when you can acquire! So many opportunites for adaptation via acquisition, and as we can read from papers cited in this blog that it is so-so easy to just transfer those genes straight across eukaryotic phyla (or from prokaryotes, why not). The age of eukaryote LGT is just now dawning, I suppose.

DAK said...

I'm probably wrong on this, but isn't also the case that Lamarck was strongly against the idea that the environment played an important role?

Anonymous said...

Doesn't cellular differentiation in multicellular organisms rely on different parts of the genome being accessed? LGT in multicellular organism would have to be not just the acquisition of coding information for novel proteins, but the incorporation of the coding genes into the genome coordinated with the phases of differentiation. It seems doubtful that the most enthusiastic LGT advocates conceive of this as a possibility.

Perhaps the more difficult issue is whether the genome of unicellular eukaryotes use a genomic structure too complex to permit of easy LGT? My impression is that the more complex structure of eukaryotes also relies on some genes being expressed at different phases of cellular development, on withholding information until needed. If so, then LGT in unicellular eukaryotes would also be rare, due to the very nature of eukaryotic organization. IF true, this would make LGT in any eukaryotes rare.

There used to be a time when automated machinery relied on punch cards (jacquard looms) or cams (the original sewing machine.) The universal Turing machine is often described as using an infinite punched tape. This seems to me a better metaphor for the genome than the activity of DNA. If you don't think of the genome as a computer sending programs but an elaborate thicket of cams/punch tapes and cards, accessing the needed template becomes an issue in complex organisms (which I think includes even unicellular eukaryotes.) The nature of eukaryote organization seems to require in this picture the excision of as much junk in the way as possible.

The usual adaptationist picture ascribes a near infinite capacity to perfect the genome. But even a more realistic assessment of the powers of natural selection implies that when vicissitudes of natural history permit, the DNA models for old traits of less value will be ruthlessly pruned. The result today would be a patchiness in the presence/absence of these primordial features. Multicelled organisms in effect insulate many of their cells from the environment by creating their own environment, called the body. Less intense pressure from the environment weakens selection pressure for excision of useless traits, so junk would accumulate in them at a different rate?

The question is, does "rare" mean unimportant in the history of life? Given that eukaryote evolution has gone on for billions of years, "rare" seems unlikely to mean never. The picture of how significant LGT is to the history of life is also a picture of the microbial world. I'm not sure that competition from other organisms would be as intense as today, meaning fewer LGT traits would be prohibitively deleterious. But in a microbial world, one would imagine the equivalent of algal blooms, where an organism with an advantage reproduces to bacterial potential. To change the metaphor, does this wipe the slate clean?

AJR said...

Wow…these Lamarckian Lateralists sound like epic dum-dums. Even worse than the Fake News media and Crooked Hillary! I’m glad I don’t know any of them…

AJR said...

But seriously, many of the points raised above have been addressed in a recent review paper by Husnik and McCutcheon and in our response to Martin’s Bioessays article:

Husnik & McCutcheon (2018) Functional horizontal gene transfer from bacteria to eukaryotes. Nat Rev Microbiol. 16:67-79.

Leger M.M., Eme L., Stairs C.W., Roger A.J. (2018) Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115) Bioessays 40:e1700242.

I think there is little point in rehashing all of the published data, the arguments made and the evidence they rely on that are already discussed in detail in the references that I have given and that Martin has given. Anyone who is really serious about getting to the bottom of the issue of the extent/validity of eukaryote LGT should read Husnik & McCutcheon (2018). If you read this paper carefully and examine all of the published work it cites (which you really should do if you want to investigate this issue thoroughly) you will find abundant evidence for laterally transferred genes in all manner of eukaryotes, many of which were clearly beneficial to the recipient organism and likely fixed by selection. One can argue that such events could not have occurred based on a priori back-of-the-envelope probability arguments without reading the papers or one can take the evidence reported in those papers seriously (if you don’t believe me then read the papers and determine what precisely is wrong with all of them). The fact is one cannot dismiss all (or even most) of these examples as artefacts or contaminants or failed phylogenies or transient non-functional events.

Regarding pan-genomes in eukaryotes. They do exist.

Read for example:
Legras et al. (2018) Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Mol. Biol. Evol. (advanced access)

Peter et al. (2018) Genome evolution across 1,011 Saccharomyces cerevisiae isolates
Nature 556:339–344

Lind et al. (2017) Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species. PLoS Biol. 15:e2003583

Read et al. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. 499:209-13

Keep in mind that we still don’t have sampling of multiple genomes from very many free-living unicellular eukaryote species, so we can’t really know whether or not pangenomes are common or not.

Regarding mechanisms. In the Leger et al. paper we cite many papers that discuss potential mechanisms in detail (inter-kingdom conjugation, viral transduction, gene transfer from endosymbionts). If one still finds it hard to believe that genes can get moved around between eukaryote genomes, then consider the rate of discovery of new eukaryotic viruses lately -- it is likely that we have only found the tip of the iceberg. Consider for example, a recently described giant virus in the green alga Tetraselmis (Schvarcz CR and Steward GF (2018) A giant virus infecting green algae encodes key fermentation genes. Virology 518:423-433). Two of the host-derived genes encoded in this virus are in fact involved in anaerobic pyruvate metabolism (pyruvate formate lyase and its activating enzyme). These are the same genes as found in anaerobic protists functioning in their mitochondria (see Stairs et al (2011) Mol. Biol. Evol. 28:2087-99 or Müller et al. (2012)). Couple this observation with the findings of chunks of integrated giant virus genomes in 66 different eukaryotic genomes (Gallot-Lavallée L and Blanc G (2017) A Glimpse of Nucleo-Cytoplasmic Large DNA Virus Biodiversity through the Eukaryotic Genomics Window. 20;9(1). pii: E17). Does this sound like a viable mechanism for moving genes from one eukaryote to another? It does to me.

In any case, I think readers who are truly interested in knowing what conclusions/arguments are supported best by the evidence really have to read the relevant literature for themselves and make up their own minds.

AJR said...

I inadvertently failed to provide complete references for two papers above:

Gallot-Lavallée L, Blanc G. (2017) Viruses. 9(1). pii: E17. doi: 10.3390/v9010017.

Read et al. (2013) Nature 499:209-213. doi: 10.1038/nature12221

Rosie Redfield said...

Am I right in thinking this is all beside the point of whether LGT is 'Lamarckian'? That would require that the processes that cause LGT preferentially transfer adaptive changes.

AJR said...

Yes, I don't think any of the argument above is truly about whether or not LGT is 'Lamarckian'. Anything we have written about the subject has always relied on the assumption that, immediately after acquisition, new genes in eukaryotes could be neutral, deleterious or beneficial. I certainly do not think that the processes involved in LGT preferentially transfer 'adaptive' genes (although it is possible that adaptive genes are present at a higher frequencies in environments in which they might be useful).

Federico Abascal said...

LRRC8 and pannexin genes have been likely horizontally transferred between chordates and Nematostella (Cnidaria). It's that or a very intrincate combination of multiple gene losses along multiple branches of the metazoan tree.

John Harshman said...

One ought to be able to investigate this by comparing the amount of divergence in these genes with the amount in other genes, assuming that horizontal transfer happened much later than the divergence of lineages.