Friday, July 19, 2013

What Should We Teach About the "Tree of Life"?

As most of you already know, I think the Three Domain Hypothesis is dead. The history of life is better explained as a net with rampant transfer of genes between species [The Web of Life]. This idea has been widely promoted by Ford Doolittle.

The debate over the tree of life has implications concerning the distinction between "prokaryote" and "eukaryote." I was checking some recent papers and came across one by Doolittle and Zhaxybayeva (2013) that seems particularly relevant. They discuss the evidence for and against the division of life into three domains and the attempt by Norm Pace to band the word "prokaryote."

The authors point out, once again, that eukaryotic genes are most closely related to genes from cyanobacteria, proteobacteria, and archaebacteria, in that order. The majority, by far, have their closest homologs in bacteria, not archaebacteria. The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium plus genes transferred from mitochondria and chloroplast to the nuclear genome.
Why, if the Archaeal signal is the weakest, is the Archaeal/eukaryote sister relationship enshrined in textbooks, and the concepts of paraphyly employed so enthusiastically by Pace in his effort to discredit “prokaryote”? Of course, even if the preponderance of data were all that mattered, prokaryotes would still be paraphyletic, with eukaryotes seen as sisters to the Cyanobacteria or Proteobacteria. But the more we come to see eukaryotes as a chimeric clade, established by symbiosis, cell fusion, and LGT, through the active participation of several or many prokaryotic lines, the more aptly descriptive the “eu” and “pro” in “eukaryotes” and “prokaryotes” begin to look.
Theme

The Three Domain Hypothesis
They point out that biologists have a tendency to simplify and the simple Three Domain Tree of Life satisfies a natural urge.
And yet, such natural kind thinking comes naturally to biologists, generating much of the heat in our arguments. Insistence that the grade distinction between prokaryotes and eukaryotes must be discarded because it conflicts with the division of living things into clades reflects a belief that “the one true taxonomy of the universe” is the Tree of Life—to which concept, as loyal Darwinists, we feel we must cling. And yet, because of chimerism and extensive LGT, that Tree means much less as a description of what organisms are like and how they came to be that way than Darwin himself would have ever imagined (Doolittle 1999; Martin 2011).

Furthermore, the Tree unambiguously depicts three discretely defined monophyletic clades if and only if we accept as settled many highly arguable propositions about how evolution proceeds, about what the data say in that regard, and about how classification is properly to be pursued. Some of these propositions, reviewed here, are that (1) in spite of the testimony of most of their genes, the “one true” way to look at Eukarya is as sisters to or emerging from within Archaea; (2) in spite of very sophisticated recent analyses of those genes thought to be most truthful, sisterhood (rather than emergence from within) is the right way to understand this relationship; (3) Bacteria and Archaea are themselves properly described as monophyletic clades, even though it is but a few percent of their genes that tell us this, with the preponderance of genes saying that they comprise a single, albeit highly structured and admittedly very slowly mixing population; (4) that it makes sense to speak of LUCA, either as a single cell or species or (alternatively) as a heterogeneous population extended over time; (5) that it makes sense to describe LUCA (of whatever type) as something other than a prokaryote. None of these is provably wrong, but none will ever be proved right, and all are matters of opinion, not fact. Definition-dependent, supposedly logic-driven arguments on the use of “prokaryote” seem doomed to failure by the same criteria with which they are undertaken, coupled with the vast underdetermination of any of our current theories about early cellular evolution (Vesteg and Krajcovic 2011; Forterre 2011).
Most biologists haven't thought very much about this issue and that's especially true of those who teach undergraduate courses. Let's think about the ones who are up to speed. They realize that the simple tree of life is probably wrong or, at the very least, seriously misleading. Should you tell undergraduates that the history of life is a lot more messy that what they learned in high school?

Here (below) is an example of what scientists are teaching in undergraduate classes. This is a lecture by Jonathan Eisen—an expert on phylogeny—given to a class of undergraduates in the Fall of 2012. It presents the case for three domains in the strongest possible terms. Students are not told about any alternatives.1

I ask a serious question ... is this what we should be teaching undergraduates? Is the real biology too complicated for them? Is it okay to simplify even if we know that we are misrepresenting the truth?



1. There are very few characters that are exclusive to eubacteria and/or archaebacteria. For example, many gram negative bacteria have lipids with ether linkages and most eubacteria have DNA binding proteins that organize their DNA into complex supercoiled, looped, structures.

Doolittle, W.F. and Zhaxybayeva, O. (2013) What Is a Prokaryote? The Prokaryotes: Prokaryotic Biology and Symbiotic Associations, 21-37. [doi: 10.1007/978-3-642-30194-0_114]

57 comments:

  1. The "Tree of Life" is still a useful concept, within certain bounds. It's a great tool for explaining why evolution is true, though I have never seen a school use it.

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    1. How could a false concept be a useful tool?

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    2. So you're opposed to teaching Newtonian mechanics in physics classes?

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    3. @Jerseyboy

      Glad to hear that you are now opposed to the teaching of false concepts.

      That is a refreshing and welcome change of world view on your part.

      Welcome to reality.

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    4. Steve,

      Can you be more specific, please? I'm afraid you lost me. I am sorry, if I have missed any of your other comments that may have implemented me.
      JB

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    5. Because no matter what, the majority of genes are transferred vertially, not horizontally. For most of that kind of evolution "normal" people think about, that is, plants and animals. Humans and their dogs and cats, cows, flowers etc. For those organisms, the tree of life is actually pretty solid and indeed pretty much a tree.

      Of course, as people who really know biology knows, most of the evolution that has taken place on this planet has happened in single-celled organisms. There the "tree of life" is a web, it only "trends" towards a tree.

      So, by analogy, teaching people newtonian mechanics(a useful approximation) is like teaching them about the "tre of life". See:
      Seeing the Tree of Life behind the phylogenetic forest
      Pere Puigbò, Yuri I Wolf and Eugene V Koonin*
      http://www.biomedcentral.com/1741-7007/11/46

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    6. Just to make sure I'm not misunderstood, I'm not saying we shouldn't teach them that the tree of life is a web, we should. But the concept of a tree can be taught, and where and why it applies and where and why it doesn't. That would be teaching the facts.

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    7. Part of my comment was lost. I was referring to using the nested hierarchy in K-12, and necessarily in undergraduate when that fails. The concept of the nested hierarchy had never completely occurred to me until John Harshman pointed it out to me many years ago on Usenet.

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  2. Teaching the tree of life definitely misrepresents the truth, but so does the teaching that there was only one LUCA and, for the same reason, that there was only one origin of life, I think. The paper speculates so much, that any interpretation, in light of the evidence, or lack thereof, can be misleading or simply false.

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    1. I think that 10^2860 is a high enough probability for scientists to use the term "certainty" with regard to LUCA. Of course, if the arguments ever suggest otherwise I am willing to revise my conclusion. Pray, tell, what is it you do under those circumstances?

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  3. My old evolution instructor, Charlie Thompson, used to say that education is a process of carefully controlled lying. I think that applies well here. The tree concept is useful at all levels, even at the root, even if it's multiple superimposed trees.

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    1. Clearly there are limits to carefully controlled lying. I think this is one of them, especially at the undergraduate level in university biology courses.

      I strongly suspect that the vast majority of teachers who teach the Three Domain Hypothesis as gospel, are not lying.

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    2. @John Harshman,

      One of my professors of psychology, old-school with up-to-date knowledge, claimed that "it is not a lie, if YOU believe it." He told me, that mentally ill people have been able to beat the lie detector test, just because they believed in everything they had been asked. However, he did say that Darwin would fail this test as would most of Darwinist/ Evolutionist and possibly creationists-just because there is no real consensus among them as well. This forum is a very good example; nobody really knows what modern evolutionary theory is, but I god lectured each time I ask. It’s just different each time. How is that science?

      PS I love science; the real one

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    3. @Larry "I strongly suspect that the vast majority of teachers who teach the Three Domain Hypothesis as gospel, are not lying."

      Why? Because they don't know better?

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    4. Why would anyone care what an 'old school' psychologist said about 'Darwninst/evolutionist'?

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    5. Sam Harris,
      "Why would anyone care what an 'old school' psychologist said about Darwinist/Evolutionist'?"
      Of course, if your beliefs don't align with his... It's all about self-interests. Didn't you know?

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    6. Of course, your "beliefs" align with denying evolution, so of course you take what your psych professor declared about evolution as Gospel, since it aligned with your faith. Pretty transparent.

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  4. A related question is how to draw the tree/web of life now in books and articles. I ask for very selfish reasons! ;-)

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    1. In the last edition of my book I used a version of the web of life drawing from Doolittle's 2000 Scientific American article. It's similar to the one you used on page 114 of your book.

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    2. I would love to teach my kids evolution. I can't. Because supposed authorities in the field can't agree even on little things. What's the problem? Where is the problem? IS THERE A PROBLEM? Frankly, I'm confused. Should my kid be confused? I bet for now.

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    3. Give it a rest, Jerseyboy. You are trying way too hard not to come across as a concern troll of sorts.

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    4. Really? What are you trying to come across as? Someone who knows something but really knows nothing? Give me something I can confirm? What is your faith based on? How did life start-I want science and not religious answer. Come on! Don't disappoint me and others!

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    5. This creationist feigning-to-be-confused moron is getting tiresome.

      Is anyone even in doubt about this particular and specious individual? His "strange" confusion about problems that just so mysteriously happens to relate with anything that touches on evolution, atheism and/or morality and humanism - is more obvious and transparent than intergalactic vacuum is to neutrino radiation.

      It really is curious how many different individuals of this specific type that end up on this blog. Or mabye they're mostly the same idiot posting under a new acronym. Hmmm... ?

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    6. What I really find amusing about jerseyboy is that he thinks that discussions between scientists about the meaning of the details of their work is somehow indicative of a failure of the scientific method, or that they are "not doing science" if they do not have absolute certainty about how new discoveries in their field should be understood.

      He probably assumes that all knowledge should be handed down from on high, and received without comment. As if that happens even in religious scholarship. Last I checked, there were innumerable religious sects which could not agree even on basics.

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    7. It's the basic theist double standard. If you're not a scientist, then any science you understand to be true is 'scientism' and you merely have a faith position, but if you *are* a scientist, you're a member of a priesthood and speaking in a hidden tongue known only to fellow-believers.

      What I find amusing about that is that the scope of the ambition of that claim is 'you're as deluded as we are'. It's not claiming superiority, merely parity. It's accusing us of being confused because we have faith and priesthoods.



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  5. Interesting. When I teach my seniors Microbiology, I present this "prokaryote or not" debate, and let them come up with their own arguments pro and con. The blog entry, and the Dolittle paper, should be very useful. Thank you.

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  6. So I am going to try to not be too defensive here as I agree with many of Larry's points but not all of them. Some comments.

    1. In the first lecture on our course we discuss how phylogenetic trees are oversimplifications of much more complex evolution.

    2. After the three domain tree is presented we also discuss endosymbioses in eukaryotes and lateral gene transfer across all organisms as reasons why a single tree of life is not the perfect representation for the evolution of life.

    3. In lab for the course we have a major section on lateral gene transfer among bacteria and how even closely related strains can have massive genomic differences.

    4. I am sure 1-3 is not enough for Larry. But I find it works well in teaching the course. I do not think there is any good evidence that we cannot refer to groups of bacteria as clades or groups of archaea as clades or groups of eukaryotes as clades. Yes, LGT makes a mess of things in some ways. But overall, I think there is meaning in discussing "cyanobacteria" as an entity and "bacteria" as an entity and "eukaryotes" as an entity. Should we discuss "archaea" as an entity? There is certainly more and more evidence that we should not. In Q&A and discussion sessions for the course we did discuss this issue and I even told them that archaea may not be a real entity. But I also said "sometimes we are going to oversimplify things" and we said that over and over. And I also said that sometimes we introduce first the oversimplification and then discuss the complexity. So the lecture here is in part such a case. After that lecture we then introduce endosymbioses, lateral gene transfer, hybridization and such and thus why a single tree is not the ideal.

    5. As a side point perhaps, I do not view the point of our course to teach specific facts but to try and teach how to think about biodiversity, organismal biology, and evolution. We discuss repeatedly in the course why a phylogenetic perspective is useful and how it can be useful and included in that is a discussion of gene transfer, hybridization, endosymbioses and other factors that make history NOT be a single tree. We teach about how phylogeny can be useful in studies of uncultured microbes, about how phylogeny can be useful in forensics, in studies of co-evolution, in studies of pathogens and disease, and much more.

    6. Again, I could defend on and on. But I should note that I disagree with Larry on the extent of the limitations of a "tree" view vs. a web view. I think a tree view for microbes still has many many uses. And that is what we want the students to understand.


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    1. Are you mentally retarded? Aren't you supposed supposed to be a scientist and no fairy-tale-teller? What kind of scientific statement is this? Basically, one can believe in anything he wants, as long as my "scientific view" is not effected.

      I once asked a very prominent scientist, possibly working at the Canandian CIA called, CSIS, why he believed in the evolution/abiogenesis. He told me this after his "ex" had been wrongly accused of an attempted abduction and murder that were pinned on her due to some "scientific evidence".

      His response was: " I believe in science; I trust science."

      No further comment.

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    2. Are you mentally retarded? Aren't you supposed supposed to be a scientist and no fairy-tale-teller? What kind of scientific statement is this? Basically, one can believe in anything he wants, as long as my "scientific view" is not effected.
      It seems you're the retarded one. None of these veiews were expressed in that post.

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    3. "Are you mentally retarded? Aren't you supposed supposed to be a scientist and no fairy-tale-teller?"

      The deceptive creationist projects.

      Why are so many of these "honest, God-fearing" zealots like this?

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    4. Why are so many of these "honest, God-fearing" zealots like this??

      Just a few, I think, but those individuals are very industrious.

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    5. Jonathan,
      I wonder if you could elaborate on the discussion of "archaea" as an entity? or just point me and other readers to a good recent reference on this? I certainly use the Woesian (sp?) tree in my micro class as a jumping off point, and discuss the shrublike aspects, and discuss whether species makes sense as a category for microorganisms, in the context of LGT. I would like to be able to go further with this, especially in my more advanced courses. When I'm teaching about this, I find that most students really like reading about the debates and arguments among scientists on these topics. Things like LUCA and deep phylogeny really get them interested.

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  7. This gets complicated in any departmental setting, by the way. When I came up for tenure, I had one colleague (who is decidedly not a fan of yours truly) make the "accusation" that I was teaching the students that the term "species" had no meaning among bacteria and archaea.

    Well, I showed how the definitions were different, both in terms of "cut-offs" and in terms of HGT/LGT.

    It was one of several things I had to defend (like the statement that I had taught students that bacteria had a cytoskeleton, which the colleague stated "was not true and nonsense"---I had to produce a ten year old review paper on the bacterial cytoskeleton to quiet that one down).

    My point? It's not just the students who struggle with the concepts. There needs to be a serious reevaluation of biology through microbial glasses, to be honest.

    Anyway, I appreciate this discussion; it will be useful in my Fall course.

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    1. If you ever want to have a really deep discussion about "species:" John S Wilkins.

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  8. Within eukaryotes, are we misleading people by saying that there is a phylogeny that is a tree? Of course there are hybridization events -- and didn't we always know about that? And there is some horizontal gene transfer, and introgression events. So we've always known that the tree isn't exact.

    But it's generally there and generally useful.

    What I found extremely annoying are the statements from Ford Doolittle and from the late Carl Woese saying that there just is no tree, nosiree, nada, zip. none whatsoever "at least in prokaryotes". And immediately creationist web sites put up those quotes, leaving off the qualification, trying to convince their readers that evolutionary biologists had always been wrong when they argued that there was evidence for the genealogy of life being treelike. And Doolittle, Woese and their coauthors did not attempt to clarify the situation. Which seems irresponsible to me.

    Am I wrong about that? Have they made everything clear, or are Ford and co. still arguing that there just is no tree?

    As to the issue of how many domains of life there are, that seems to be more a matter of the formalisms of classification than of disagreement about evolutionary history.

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    1. Interesting, in a recent paper (http://www.ncbi.nlm.nih.gov/pubmed/23479647) Doolittle says: “the most heated arguments in biology are not about facts at all but rather about the words that we use to describe what we think the facts might be”.

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    2. I personally find the 'Woesean' notions of 'genetic annealing' gradually coalescing into vertical descent to be thoroughly unsatisfactory. A phylogeny consisting of 'true' vertical descent with an occasional drip of LGT would, over deep time, become quite scrambled, but this does not justify the inference that, once upon a time, lateral transfer is all there was. This is a scenario that flies in the face of evolutionary logic, to me, as I see linkage of genes in multifunctional evolutionary 'alleles', replicated as a piece, as an essential precursor to cellular life, and indeed to adaptive evolution. This linkage unit could extend, by fragment incorporation or internal duplication, but I don't see how viable genomes can arise by cobbling together a temporary mix of fragments. Without linkage, and replication for all, what's in it for them?

      Further, even setting aside Theobald's statistical test of single ancestry, no plausible explanation is offered as to how, if LUCA were not a single organism, the 50-odd invariant codon positions came to be universal.

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    3. Joe, Claudiu, Allan - I'm in full agreement.

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    4. I'm sorry to hear that Rosie. You're much more interesting when you disagree.

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  9. Joe,

    Why would you mislead anybody? Are you a scientist? If you are one, what kind of profession is " a misleading scientist" and who pays for or it?

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    1. Jersey - are you a creationist or ID advocate pretending not to be? It seems pretty obvious, Now please give it a rest.

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    2. I'm neither, as I only follow the evidence, wherever it may lead me.

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    3. Then you shouldn't be having any problems. This discussion is about how to best present that evidence, not about whether evidence exists. Your confusion is of your own making.

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    4. Jerseyboy

      What exit?

      If you are really from Jersey, you know what I'm asking.

      If you are another sock puppet for the banned Vashti/Witten, you don't.

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    5. "I'm neither, as I only follow the evidence, wherever it may lead me."

      Right... And let me guess - it amazingly leads you to Yahweh?

      Pathetic.

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  10. Sorry but to a lay person this debate is confusing because all the trees appear to define single celled "species" genetically, which is a problem because lateral gene transfer blurs those lines. But the biological species concept really defines species reproductively, doesn't it? In bacterial fission, the membrane is simply divided. Is this reproductive continuity part of the notion of a unicellular species? I would think those species lines are still blurry because of symbiosis and evolutionary change, but it doesn't seem like the original unicellular "tree of life" collapses into a kind of felt. What is the standard notion of unicellular species?

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    1. The biological species concept is reproduction-based in the sense that sexual intercompatibility draws its boundaries. It only applies to sexual eukaryotes. Asexuals should more nearly approach the 'tree ideal' - eukaryotic sex is a kind of wholesale LGT, though sexual speciation remains tree-like.

      When you replicate any DNA base pair, you get two. Those can be further replicated, and you end up with a 'tree' for each bit. Any two descendants at the twig-tips can trace back to a node at which their ancestral bases were paired in the same DNA molecule.

      Neighbouring bases should follow the same pattern, so you would expect to be able to superimpose the trees from two close neighbours. And if replication were perfect, and gene transfer nonexistent, it would be trees all the way down. But obviously, there are confounding forces at work when you try to infer the actual phylogeny from modern material - mutations, deletions, duplications, LGT fragment incorporation.

      Because it derives from a fundamental property of the genetic material, the 'ideal' phylogeny would be treelike for any base, and if the whole genome is replicated, the same tree will apply across the genome. But with LGT, threads connect different branches. At the level of the individual base, passage from one lineage to another does not invalidate the tree concept at base level, but blurs it at genome level. A lot of this (and gene loss etc) over time makes the 'vertical', idealised tree harder to recover from any dataset.

      Some authors hold that this net-effect is not simply an artefact of vertical descent + a dripfeed of LGT + time, however.

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  11. PS It occurs to me that we could imagine that a molecule from a LUCA has somehow escaped dissolution and is still incorporated in a plasma membrane!

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  12. Well, speaking as a very non-educator (and one of those confusing people whose elliptical delight in extraneous details and apparently nonessential digressions makes following their conversation in person especially a stress test for your short term memory even at the best of times; I cop to this as warning about the taste I'm expressing, here, for what it's worth; you think mapping out ancestry is complicated given LGT, try parsing my grammar), I find the whole messy, complicated thing that's emerging here way, way too fascinating _not_ to tell people as soon as possible. That'd be like ripping them off...

    ... but I think you need to explain the 'tree' picture at least as a historical thing/simplified/approximation of reality thing. Because any student has probably heard of it even outside bio courses, and if you don't explain the status of the thing upfront, you're probably just going to have to take it in Q&A anyway, eventually, and it _is_ significant from a history perspective, at the very least. But I think you want to say upfront: you'll hear this term, you'll see these tree things; oh, but by the way: that can't really represent exactly what's going on, here.

    I don't think it's really so horribly confusing. Just tell them: here's the deal: genes move between genomes and organisms all sorts of messy and complicated ways, and assuming it's all divide divide divide and thus branch branch branch just isn't how it is. Prior to the realization of the significance of LGT, it made sense to see the whole thing as a tree, but it never was that, exactly. Genes, they can get around, trouble is... Draw them a nice little picture; here's a cell membrane dividing, dividing, dividing... Here's the genome inside as a pile of semi-coherent bits sometimes going along, dividing in synchrony with that... And here's a snippets of nucleotides coming in from another membrane entirely, that divided from this one quite a long while ago. And what do we call that?

    We call it life, messy, complicated, fascinating life. We call it the reality the sequencers are revealing. Oh, and listen, as a eukaryote yourself, you really should have a proper appreciation for this, you messy mosaic of bits and pieces, you... Honestly, I've always found that aspect of our own biology strangely charming, myself.

    (Even strangely fitting. Frankengenomes 'R us.)

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    1. I largely agree, and it turns out that the "problem" here isn't all it's made out to be. The web of life in single-celled organisms still tends statistically towards a tree.

      In any case, I don't see any issue with just teaching the facts here. Trees are fine for humans, dogs and other large multicellular eukaryotes for the most part, but most of evolution has happened in single-celled life where it's much more messy and life a web(though still tending statistically towards a tree). As long as it is explained how and why these concepts apply and where they apply.

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  13. I am not really qualified to judge prokaryote phyogenetics so I don't really take a position on the three domains controversy. And for all I know it might be correct that there is so much LGT going on. But that being said:

    First, I know that there are people who are more qualified than I am and who argue that at least a good deal of the mush that is interpreted as being indicative of rampant LGT might stem from the difficulty of establishing sequence homology between lineages that diverged from each other a really really damn long time ago. The host of this blog has written about the problem himself, of course.

    Second, just because there is LGT or introgression even between Eukaryote lineages does not mean that there is no tree. We systematists and phylogeneticists are, after all, not interested in producing a classification of gene copies, we merely use them as data. What we want to produce is a classification of species, and species can still form a mostly tree-shaped species phylogeny even if there is some gene flow between them.

    In other words, the history of a species is not equal to the history of its genes, and to think otherwise is to succumb to the fallacy of composition.

    Finally, ...

    The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium

    It is clear that we have very different visions of what "most likely" means. To me it sounds too much like this. But again, I work on flowering plants, not on the really deep phylogenetics.

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    1. Second, just because there is LGT or introgression even between Eukaryote lineages does not mean that there is no tree

      Let's assume that there IS a tree buried somewhere in all that data. Are you absolutely certain that it will show eukaryotes as a sister group of Eocytes? If you are not certain, would you teach it anyway?

      In other words, the history of a species is not equal to the history of its genes ...

      Exactly. That's why it's wrong to teach that eukaryotes are most closely related to Eocytes just because a small subset of genes shows that phylogeny. Don't you agree?

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    2. As I said, I have no opinion on this specific question and I am not teaching or researching anything beyond the flowering plants anyway. I am merely afraid that some readers might be prompted to throw out the baby with the bathwater if they get the impression that LGT means the absence of tree structure. Some people make the same argument even for within the plants or animals, where LGT is definitely much less frequent than in bacteria.

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  14. I think that a Tree of Life (or more accurately a Shrub of Life) works well for Eukaryotes, despite a relatively small amount of lateral gene transfer. I've taught it and would again. I think arguing about the value of this Shrub is like pointing out the problems of using a 2-D photograph to teach about a 3-D house; the limitations are real, but the photo can still provide a good first approximation of the truth.

    With regards to prokaryotes (a useful descriptive term, though not a clade), I've taught a kind of Shrub of Life with the eukaryote nucleus evolving within Archaea. I've commented that lateral gene transfer makes the picture messy. If I were teaching this again, I'd emphasize the messiness even more, the eukaryote nucleus as a chimera. (Reading Sandwalk is useful.) I like these topics where I can say, "This is the best I know now but this is an area of active research." (I often have to say, "This is the best I know but I don't know much," so it feels good to have a reason to not know.) Some of the students aren't happy with the uncertainty but it's good for them.

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  15. In their article entitled “What Is a Prokaryote? The Prokaryotes: Prokaryotic Biology and Symbiotic Associations” Doolittle and Zhaxybayeva write:

    “At issue is whether living organisms on this planet are two kinds (prokaryotes and eukaryotes) or instead, three (Bacteria, Archaea, and Eukarya).”

    We have known now for many, many years that viruses are the most abundant life forms on this planet, and that the repertoire of viral genes is greater than that of cellular genes. Interestingly, there is an article just published in Science (http://www.sciencemag.org/content/341/6143/281.abstract) describing some very large viruses (Pandoraviruses) which have a genome larger than those of some protozoa.

    Therefore, not including viruses in the discussions on the Tree of Life (ToL) is poor science any way you look at it. Maybe it is time for people who write, with apparent authority, about the kinds of organisms on our planet and about the ToL to take a refreshing introductory course in Biology.

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  16. Isn't there a point in time after which the Tree of Life becomes a true representation of particular clades? Is it that big a deal to admit that before that time, with a lot of horizontal gene transfer and so forth, that things are a lot messier? I think undergraduates ought to be able to handle that.

    "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one;" or, for that matter, into many.

    Does it really matter if the lines of descent are somewhat blurred up to a point?

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  17. Paper in Nature today arguing for two domains, archaea and bacteria:

    http://www.nature.com/nature/journal/v504/n7479/full/nature12779.html

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