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    What The Platypus Genome Is And Isn't
    By Michael White | May 9th 2008 02:46 PM | 48 comments | Print | E-mail | Track Comments
    About Michael

    Welcome to Adaptive Complexity, where I write about genomics, systems biology, evolution, and the connection between science and literature,

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    I haven't contributed a single thing to the platypus genome project, but since my desk sits one floor above where people and robots broke the platypus DNA into chunks, cloned those chunks into bacteria, sequenced the pieces of DNA, and used massive amounts of computing power to assemble the stretches of sequence into a complete genomic whole, I'm going to consider myself somewhat of an authority on the subject and tell you what's wrong with other people's ideas about the platypus.

    The genome sequence of the platypus was published Thursday in Nature, and from the press headlines, you could be excused for thinking that genomics has in fact confirmed that the platypus is a freak of nature: part bird, part reptile, and part mammal. The animal certainly looks like it - the platypus has the webbed feet and bill of a duck, and venomous spines and rubbery eggs that remind us of reptiles, but it has fur and feeds its young with milk, so it must be a mammal. The confusing press headlines might even lead you to believe that we sequenced the platypus genome just to figure out what this thing is, when the truth is, as we'll see below, that the genome sequence has essentially confirmed what evolutionary biologists have already deduced about the position of the platypus on the tree of life.

    Is the platypus part bird, part reptile part mammal, an amalgam of very different groups of animals? Is it a primitive mammal that resembles the early ancestors of all mammals? Can we figure out just what this creature is by gazing at its genome?


    Photo Credit: Stefan Kraft, courtesy of the Wikipedia Commons


    The Platypus is a Genuine Mammal, not an Amalgam

    The platypus Ornithorhynchus anatinus is part of a group of mammals known as Monotremes, who last shared a common ancestor with us between 160 and 200 million years ago. At that point, one mammalian line split off to give rise to today's monotremes, while another eventually led to the marsupial and placental mammals. What this means, of course, is that the platypus is as distant from that ancient ancestor as we are - humans, kangaroos, and platypuses are all modern mammals.

    However some traits of the platypus can be considered primitive, if you take primitive to mean 'resembles the ancestral form' (instead of the more colloquial meaning 'less advanced'). The most obvious example is that the platypus lays eggs, something which ancient mammals also did, but which most modern mammals no longer do. Egg-laying is an ancestral trait that has persisted in this particular evolutionary line, a trait which the platypus inherited from the egg-laying, reptile-like ancestors of all mammals - in that sense, it's primitive.

    Other features of the platypus aren't primitive, and have absolutely nothing to do with the fact that all mammals shared a common ancestor with today's birds and reptiles. The venomous spines possessed by the male platypus are not there because of some reptile ancestor that had venomous spines; early mammals probably had no venom, and evolutionary biologists have long insisted that this interesting platypus feature is likely an independent evolutionary invention. Venomous spurs are no more reptilian than the human lack of fur: we don't have fur, and our reptile ancestors didn't have fur, but our bare skin is not a trait inherited from fur-less reptile-like ancestors, it's a trait we lost recently in our evolutionary history.

    The same is true of the 'duck bill', which has nothing at all to do with any ancestors the platypus (and all mammals) share with birds: it's a separate invention, a highly developed electrical sensor that the platypus uses to search for food, much like the bill of a paddlefish (which is also an independent invention). Despite the bill and the webbed feet, the platypus is not "part bird" (as USA Today proclaimed), and its flat tail does not make it part beaver either (beavers are placental mammals, more closely related to us than to a platypus).

    The platypus is not part anything: it's 100% mammal, with some primitive traits of ancient mammals, like egg laying, and a few newly invented traits like the bill, the webbed feet, and the venomous spines.

    The big story hidden in the platypus genome is that evolutionary biologists were right about what the platypus is: by looking at its genome, we can see which platypus traits are ancestral, and which are new inventions (derived is the proper term), only now in much more detail because we can see how the genes involved changed.

    Gazing Into The Platypus Genome

    So what can we learn about this critter by gazing at its genome? By making the right comparisons, we can figure out which genes were in the shared ancestors of birds, reptiles, and mammals, but which have been lost in the line leading to marsupial and placental mammals. Below you can see the evolutionary relationships between major groups of mammals, as well as birds and reptiles. For each of these major branches, except reptiles, we have at least one good genome sequence, which I've indicated in the figure. (The Anole lizard genome sequence is in progress, so right now we have to make many of the key evolutionary comparisons with the chicken genome.)



    The comparison works like this: If a particular gene is present in the platypus and the chicken genomes, but not in other mammal groups, then we conclude that this gene was present in the shared ancestor of all these groups, but was at some point lost in the line leading to marsupial or placental mammals. Or, if a gene is present in the platypus, but not in other mammals or birds, then we conclude that this particular gene was not present in that shared ancestor of all these groups; it was newly derived at some point in the evolutionary line leading to monotremes. Of course, there is an alternate explanation: that same gene could have been present in the last common ancestor, but lost in birds, marsupials, and placental mammals, which is less likely but still possible. You get the picture - with the right set of genomes in hand, one can make all sorts of comparisons like this. (And, just to clarify, when I say gene here, I also mean variants of a gene, or any other genetic feature we can look at in the genome.)

    By doing this, we can find genes for ancestral mammalian traits that are preserved in the platypus, but which have been lost in marsupials and placental mammals. Genes contributing to egg-laying are the obvious candidates, and in the platypus genome we find several genes involved in egg development that have previously only been found in fish, birds, and reptiles. What this means is that these particular genes, present in the early ancestors of all mammals, were lost in marsupials and placentals, but preserved in the monotreme line. Before the genome sequence came out, the story evolutionary biologists would tell you was this: egg-laying is a trait that's been preserved in monotremes in an unbroken line from early egg-laying ancestors, while the rest of the mammals lost that egg-laying ability. And now the genome sequence bears this story out.

    We can find another example of an ancestral trait in the platypus genome: the sex chromosomes. While humans have one X chromosome (although you may have two non-identical copies of this particular X chromosome), the platypus has 5 - that's right, 5 X chromosomes. These X chromosomes look nothing like the human one; instead, they resemble the sex chromosomes of birds (and probably some reptiles, but we have less sequence data for reptiles). Again, this is probably another example of the ancestral state being largely preserved in the platypus. The last common ancestor of birds, reptiles, and mammals probably had a similar sex chromosome setup, but in the evolutionary line leading to marsupial and placental mammals, that setup has changed significantly.

    The Independent Invention of Venom

    What about venom? Few other mammals have venom, and the most plausible evolutionary scenario is that early mammals did not have venom - it arose independently in the platypus, and not by inheritance from a venomous reptile ancestor. Again, what we find in the genome supports this scenario: the platypus does not have the exact same venom genes found in reptiles, meaning that the platypus did not inherit its venom-producing ability from an ancient venomous ancestor. Platypus venom is a great example of what biologists call convergent evolution, the independent evolutionary invention of similar traits in different groups of animals.

    The platypus genome confirms this independent invention story, but with a very fascinating twist: there is a set of non-venom genes which have been recruited at least twice in evolutionary history to make venom genes: at least once in reptiles, such as poisonous snakes, and once in the platypus.

    To understand what's going on here, you need to know what venom is made of. Venom is largely a mixture of various proteins that do nasty things to the prey or competitors of venomous creatures. The genes coding for these venom proteins are very similar to, and actually derived from hormone gene families, such as one family called 'beta-defensin'. We have beta-defensin genes, which make up part of our immune system. Reptiles and the platypus also have these genes. In venomous reptiles, some of the beta-defensin genes have been modified to make venom. What the platypus genome shows is that at some point in the non-venomous evolutionary history of the platypus, beta-defensin genes were again recruited to make venom, just as they were in reptiles, but in a completely independent event.

    In other words, platypus venom is not primitive; it's not a reptilian trait that the platypus inherited from the last common ancestor shared by mammals and reptiles. Contrary to what you may have read in the press, venom genes are not signs of a link between the platypus and reptiles. Here is the evolutionary tree researchers produced from the sequences of beta-defensin genes (you can read Ryan Gregory's great primer on how to read these trees):



    Figure 4, Nature 453:180, published under the Creative Commons License


    This tree shows, based on the sequence data of the genes themselves, that the platypus beta-defensin genes descend from the ancestor of all mammals, and not from a venomous reptile.

    So the genome sequence tells us what biologists have been saying all along: the platypus is not evolution's Frankenstein, not an amalgam of spare parts from different species. The platypus is a marvelous example of how evolution works, preserving useful traits through long stretches of evolutionary time, while also inventing new traits, sometimes over and over again from the same raw materials in very different lineages. That's as true of our history as it is of platypus history.

    But is this why we sequenced the platypus genome, just to learn about its evolutionary story? I'm a big advocate of answering basic research questions like this, yet this is not the only valuable aspect of the platypus genome. One of the best ways to learn about the functions of the various parts of the human genome is through triangulation, by comparing our genome with other genomes that are spaced at various evolutionary distances from ours. One case that stands out right now is that of the immune system genes in the platypus, which promise to teach about the evolution of the immune system in mammals, which in turn can shed light on how our own immune system functions and goes awry.

    The platypus may look odd, but its genome fits nicely into an already well-established evolutionary picture, and in spite of this mammal's strangeness, it has much to teach us about ourselves.

    For more on platypus evolution, and the misleading language found in both the press and the scientific papers themselves, read Ryan Gregory's take.

    Comments

    T Ryan Gregory
    SUPERB.
    adaptivecomplexity
    Thanks. I had written this thing up, and then I saw your piece - which made me scan my draft to make sure I hadn't fallen into any of the mistakes you so deftly pointed out!

    Mike

    Mike
    "The platypus is .. 100% mammal" - To say that the Platypus is part bird and part reptile is not entirely inaccurate as their Genome has just revealed. It is perhaps indeed a more accurate description than to assert that it is "100% mammal". "A draft sequence of the platypus genome reveals reptilian and mammalian elements and provides more evidence for its place in the ancestral line of animal evolution."
    http://www.nature.com/news/2008/080507/full/453138a.html
    The venom genes may have evolved independently but it shares other reptilian genes.
    How do you define an animal to be "100% mammal"? and thus how precisely do you determine that it is "100% mammal", or indeed 100% anything when the genetic relationships are so clearly revealed?

    adaptivecomplexity
    The genetic relationships found in the genome show what evolutionary biologists have long established with other evidence: the platypus, and all other mammals, last shared a common ancestor with today's birds and reptiles about 300 million years ago. In other words, we are just as closely related to reptiles as the platypus is.

    The reason a platypus has some 'reptilian features' like egg-laying is not because it is part reptile, or more closely related to reptiles than we are, it's because certain ancestral traits remained largely unchanged during its evolutionary history. Up until about 160 million years ago, all mammals were egg-laying, but our line lost that ability - along with some of the genes involved.

    Unfortunately, much of the news coverage of this, including the nature news story, is confusing on the evolutionary biology.

    Mike

    Mike
    You have said "all other mammals, last shared a common ancestor with today's birds and reptiles about 300 million years ago. In other words, we are just as closely related to reptiles as the platypus is." That inference (In other words) is fallacious - apparently we shared a common ancestor with the platypus 166 million years ago, so they could be well over a 100 million years closer to reptiles than we are.

    Rick Wilson, director of The Genome Center Washington University in St Louis had this to say "You see genes that look reptile-like, genes that look bird-like and genes that look mammal-like" and Jenny Graves, head of the Comparative Genomics Group, Australian National University said "The platypus is a very ancient offshoot of the mammal tree, so it was 166 million years ago that we last shared a common ancestor with platypuses, and that puts them somewhere between mammals and reptiles, because they still maintain quite a lot of reptilian characteristics that we’ve lost .. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having live-born young."

    I think to deny that platypus's are far closer related to birds and reptiles than we are is misleading both from the genetic point of view and from its obvious characteristics like a beak, egg laying and webbed feet. Thus I stand by my contention that to say a platypus is part bird, part reptile, part mammal is a more accurate description of the reality than your statement that it is 100% mammal. - Richard

    T Ryan Gregory
    The lineage that includes modern platypus and the one that includes placental mammals converge at a point 166 million years (or thereabouts) ago, which means that from that point backward in time they are exactly equally related to any other lineage. Think about it this way. The family line that led to you and the one that led to your first cousin converge at an ancestor (your grandparent), and then beyond that any relatedness you may have to other more distant relatives is equal because it is connected via the same line. The quote you give is, at best, poorly worded and at worst demonstrates some common misconceptions about evolutionary relationships between modern taxa.
    "..which means that from that point backward in time they are exactly equally related to any other lineage."

    I dont see how that follows. One lineage evolves and diverges greatly and another doesnt - thus the one that doesnt evolve as much is much closer genetically related to the ancestor than the one that does. This would be magnified over time.

    This is borne out by the genetic study.

    And the people who you have accused of choosing their words poorly and demonstrating common misconceptions about evolutionary relationships between modern taxa are no less than the Director of The Genome Center Washington University and the Head of the Comparative Genomics Group, Australian National University, both of whom were involved in the study.

    T Ryan Gregory

    What you are talking about is amount of change over time, not relatedness.

    The platypus, like all modern species, retains some ancestral characteristics and has some highly derived ones. Yes, the platypus lays eggs, which is primitive relative to other mammals. It also has venom and electroreception, which are derived relative to other mammals.

    Here is how one can think of this:

    Once two lineages have separated, each evolves new characters independently of the other and, with time, each will show a mixture of plesiomorphic [inherited largely unchanged from the ancestor] and apomorphic [newly evolved and thus not possessed by the ancestor] character states. Therefore, extant species in both lineages resemble, to varying degrees, their common ancestor. Consequently, whereas character states can be relatively ancestral (plesiomorphic) or derived (apomorphic), these concepts are nonsensical when applied to whole organisms. Crisp and Cook, Trends in Ecology and Evolution 20: 122-128)


    Regardless of their role in sequencing the platypus, they may have minimal training in evolutionary biology.

     

    If I understand the quote you have given from Crisp and Cook, they are saying that "character states" (a beak?, webbed feet? fur? etc) are "nonsensical" (pretty strong words) when applied to "whole organisms" (in this case a platypus). Quite a sweeping statement and I dont see how it derives from, what they have said previous to this.

    However we are not talking about "character states", or physical characteristics (why cant evolutionary biologists use simple understandable English?), though some of them may indeed be due to the genes inherited from the ancestor. We are talking about genes, which very much determine and establish relatedness between species.

    I wouldn't lightly belittle geneticists knowledge and contribution to evolutionary biology. Recently the evolutionary tree was shaken up due to the genetic study of the comb jelly fish. Eventually I think all taxa will have to be redefined on the basis of their genomic code.

    adaptivecomplexity
    We're not belittling geneticists. I work in the same department and same Center as Rick Wilson - his office is just down the hall from my desk, and I have regular opportunities to hear him speak. He would tell you the same thing Ryan and I are telling you about relatedness and phylogenetic trees.

    What he was trying to say in that quote is the same as the point I'm trying to make in this post - that there are some genes, such as certain genes involved in egg development, that have been retained both in the platypus and in birds, but which have been lost in other mammals; thus the platypus has retained some ancestral traits.

    But overall, the established position of the platypus on the phylogenetic tree is supported by the genome sequence- the platypus genome paper has a figure with that same tree that is in my post above.

    Mike

    Mike
    T Ryan Gregory
    They are saying that the notion of "primitive" applied to whole organisms does not make sense, but refers only to particular characters. No one is belittling geneticists.
    T Ryan Gregory
    "The lineage of which humans are a part is a very ancient offshoot of our mammalian family tree, so it was 166 million years ago that we last shared a common ancestor with humans, and that puts them somewhere between mammals and reptiles, because they lack a lot of specialized characters that we have gained but the ancestral amniote also lacked; for instance, they have no electroreception, no bills, no webbed feet, and no venom. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having our specialized features." - John Q. Platypus
    The key is which characters are being analyzed, and whether evidence shows that platypus exhibit a less derived form of these than humans. It is not sufficient to argue that they are "early branching" and therefore ancestral in general. A branching event is a split which is followed by varying amounts of change in particular traits in the two lineages.
    I am not sure about the quote from “John Q. Platypus”, possibly some private joke but very similar to the one from Jenny Graves. I feel a little outgunned here as I neither share the physical proximity to where some of the sequencing was done, nor indeed have any qualifications in biology or genomics whatsoever (I am an engineer – genetics is only a recent fascination). I do not have the good fortune of hearing Rick Wilson’s talks or sharing his thoughts, thus I can only go by my understanding of the situation, which is as follows:

    The genome of the platypus has only just been sequenced – it's a book that we have only just opened and full story will take some time to unfold. From initial readings it is apparent that the genome shares features with mammals, birds and reptiles. It may thus provide many clues on the story of the genetic evolution from reptiles to us.

    From the evolutionary tree that I saw on Natures page it appears much more closely related to reptiles and birds than we are. To say we are equally related to reptiles assumes that evolution follows equal rates at each divergence, which is not true. The evolutionary tree is not set in stone and is subject to constant refinement and change. The story of evolution is full of holes and gaps. The platypus genome, sharing as it does, genes in common with mammals birds and reptiles may go some way in filling in those gaps.

    And with that I will bow out of this discussion – Sincerely - Richard

    adaptivecomplexity
    Don't feel like you have to bow out! The whole point of the comments is to have a chance to discuss these things - you're not intruding or crashing any private party.

    Looking at phylogenetic trees can be confusing, which is why Ryan has written a series of articles about reading them (which he's linked to in the comments).

    But here's another key thing to keep in mind about genome sequences: they never (as far as I know, without exception) provide any surprises about where on the evolutionary tree an entire organism belongs. That is because certain small regions of the genome (such as ribosomal genes) have previously been sequenced, usually years before, giving biologists a chance to look at all of the data - fossils, morphological features, and DNA sequence data - when figuring out where an organism belongs on these trees.

    However, genome sequences do often tell us interesting things about individual genes - some of which (like platypus egg genes) may resemble the ancestral form, and others of which may be new. While some individual genes may have changed a lot, and others may have changed little in millions of years, the vast bulk of the genome, in any genome that has been sequenced, supports the phylogenetic trees that biologists publish.

    Mike
    "But here's another key thing to keep in mind about genome sequences: they never (as far as I know, without exception) provide any surprises about where on the evolutionary tree an entire organism belongs."

    I can think of two - The place in the evolutionary tree of Archaea (major major) indeed the acceptance of Archaea as a separate life form, and the comb jelly fish (major major again) - the jury might be out on this one but the Archaea didnt get its rightful place without a fight.

    T Ryan Gregory
    The subject is a bit complex and should probably be covered in a separate article, but the determination of relatedness based on genetic data is not about genetic similarity per se, but the fact that genetic insights reveal a probable branching order -- and hence phylogenetic relatedness. So yes, genomic data can be used in this way, but not as a bulk similarity comparison, rather as an indicator of who is descended from most recent common ancestors. After that, one looks at similarity as a function of degree of change since the split, but relatedness doesn't change. Put another way, branch order (relatedness) is the same, but one could have branch lengths (genetic distance, or degree of divergence) be unequal as an indication of rates of changes.
    So here's where I think the issue lies...

    It's misleading to say that the platypus has genes or features that are "bird-like" or "reptile-like," and that it has these genes because it is "part bird" or "part reptile." It's misleading because it suggests that the evolutionary path somehow went bird -> platypus -> other mammals; that these are "bird genes" that were developed first in birds and then passed on to the platypus when it evolved.

    Let's give a random name to the 300-million-year-old ancestor of reptiles, birds, and mammals; the grandpasaurus, say. It's more accurate to say that reptiles, birds, and platypi all have several genes that are grandpasaurus-like, such as laying eggs. These genes are not proprietary to birds or reptiles, and having them does not make one related directly to birds or reptiles; only related directly to the grandpasaurus.

    You do make a good point that evolution proceeds at different rates in different populations. Sharks and crocodiles are often cited as being evolutionary throwbacks because they haven't changed much over many millions of years, while other types of animals (like primates for instance) evolved at a much faster pace.

    And while the platypus has evolved quite a bit since our last common ancestral split (gaining the electrolocating duck-bill, the venomous barbs, etc.), there are other features that we might consider primitive because they resemble features of the grandpasaurus that our branch of mammals moved away from, like the egg-laying.

    However, in judging speed of evolution by gross phenotypic traits, like whether it lays an egg or whether it produces milk, is automatically assigning a value judgment to those adaptations we most readily recognize. There are likely to be very many grandpasaurus genes that we humans still have, but that the platypus ditched years ago. Those genes, however, don't necessarily make us "closer" to birds or reptiles than the platypus.

    If we start assigning value judgments about "these adaptations are 'further away' from birds/reptiles; these other adaptations are 'closer to' birds/reptiles" then we're getting out of what can be accurately classified as scientific. The only metric we can use that is not introducing value judgments about the worth of various genes and the "closeness" between evolutionarily independent species is time. Specifically, how long ago was the latest common ancestor?

    Phylogenetically, mammals and reptiles/birds are mutually 300 million years apart. Placental mammals and monotremes are mutually 160 million years apart. That means that all mammals are equally as "far away" from reptiles/birds; just as how humans, cats, and kangaroos are all equally as "far away" from platypi.

    T Ryan Gregory
    YES.
    adaptivecomplexity
    There are likely to be very many grandpasaurus genes that we humans still have, but that the platypus ditched years ago.

    You're right, there are many gene likes that - I put some numbers in this comment.

    Mike

    Mike
    T Ryan Gregory
    From the evolutionary tree that I saw on Natures page it appears much more closely related to reptiles and birds than we are.
    That is precisely why those trees are misleading! I invite you to see my posts on the topic, in which I discuss this problem: Platypus sex chromosomes and basal-equals-primitive Bad quotes about evolution and genomics
    Ok I read your page on Bad quotes about evolution and genomics, and understand what you are getting at with the story from Platypus’s side. Yes the Platypus is every bit as "modern" as we are - assuming modernity to mean total time of existence from the time of the common ancestor to now.

    But your explanation from the traits point of view completely ignores the genetic story. If the platypus shares more genes with reptiles and birds than we do then they are more closely related to them than we are. If they share more genes in common with the common ancestor then they are more closely related to the common ancestor than us. And in that sense they are more "primitive" than us.

    Homo Sapien Sapiens have evolved during the last 30 – 80,000 years? If the platypus genes have remained relatively unchanged for a 160 million years there is a wide divergence in the evolutionary patterns between us and them and in that sense they are more "primitive" than us.

    adaptivecomplexity
    If the platypus shares more genes with reptiles and birds than we do then they are more closely related to them than we are.

    The platypus doesn't share more genes with reptiles and birds than we do. Some genes, which were highlighted in the paper, have been lost in other mammals but retained in platypus, true. But the vast majority of platypus genes, 82% of ~18,500, are shared among all mammals, birds, and reptiles (although each of these genes has undergone various amounts of change in each line, and may be present in multiple copies).

    Only about 50 genes, according to table 1 in the Nature paper, are present in the platypus and birds and reptiles, but lost in other mammals.

    Far more genes, genes you need to be a mammal, are shared among all mammals, but are not present (at least in 'mammalian form') in birds and reptiles.

    We really are more genetically similar to a platypus.

    Mike

    Mike
    "If the platypus shares more genes with reptiles and birds than we do then they are more closely related to them than we are."

    "The platypus doesn't share more genes with reptiles and birds than we do."??? How do you say that?

    "Only about 50 genes, according to table 1 in the Nature paper, are present in the platypus and birds and reptiles, but lost in other mammals."

    "We really are more genetically similar to a platypus." (than to birds and reptiles I presume) - That was not my contention. What I said was that IF the platypus shares more genes with reptiles than birds (and I am willing to bet that they do) then THEY are more closely related to them than we are.

    adaptivecomplexity
    Read it again: there are about 50 genes, out of ~18,500, which are are found in platypus, birds, and reptiles, but not in other mammals. That's a tiny number. More than 50 are shared by all mammals, but not reptiles and birds.

    Furthermore, I'm trying to keep things at a non-technical level by talking about numbers of genes. Most of the genome is not made up of protein-coding genes. Again, you can make various comparisons among different regions of the genome among mammals, reptiles and birds (which they do in the paper), and you find that platypus DNA is more similar to other mammals than it is to reptiles or birds.

    That's how these evolutionary trees are drawn in genome sequencing papers - they are based on DNA comparisons, genetic comparisons, and not on fossils or morphological classifications. The DNA itself places monotremes like the platypus solidly with mammals, and not with reptiles or birds.

    It's not a matter of us here betting on what the real answer is. I study genomes for a living, I've read the papers, and use many of the same techniques of DNA analysis in my own research. I'm trying to explain what the platypus genome paper says without getting excessively technical.

    Mike

    Mike
    T Ryan Gregory
    The main suggestion here not that platypus is closer to reptiles than it is to other mammals, but that platypus is genetically closer to reptiles than humans are to reptiles. My response is that I don't think you should make that assumption, and looking at the paper, it seems to me that the platypus is quite divergent in terms of genes and non-coding sequences.
    adaptivecomplexity
    I'm not clear on which assumption you mean - that platypus is genetically closer to reptiles than humans are?

    The platypus is definitely quite divergent - they say that "most neutral sequence cannot be aligned between monotreme and eutherian genomes."

    But if anything, by just counting genes you could argue humans are more similar to reptiles - according to table S5, 86% of human genes have an ortholog in all the available amnoite sequences, while only 82% of platypus genes have an ortholog - more of our genes are shared with reptiles.

    Mike

    Mike
    adaptivecomplexity
    OK, I think I get what you're saying.

    Let's take a hypothetical scenario: many, many genes were lost in the line leading to marsupials and eutherians, but retained in the monotremes as well as the reptile lineage. In that case, all mammals would be more closely related to each other by genealogy, but the platypus and the chicken would actually have more genes in common with each other. I think this is what you're suggesting, Richard, right?

    But that's not what the paper shows, in the various examples they look at. For example, miRNA genes - more are shared between mammals, than are shared between platypus and chicken. (Figure 2 in the paper)

    If you look at the tables for orthologous groups here, you can see that there are 1,352 groups of orthologous genes shared by all mammals, but not by chicken. In contrast, there are only 132 orthologous groups present in the chicken and playpus genomes, but absent from the other mammals. This means that the platypus shares more genes exclusively with other mammals than it shares exclusively with birds.

    So our hypothetical scenario, while it makes an interesting point about relatedness vs. genetic similarity, is not what we find in the platypus genome.

    Mike

    Mike
    T Ryan Gregory
    Sure - but the issue is how many genes/non-coding elements/neutral substitutions are shared by [humans + reptiles/birds] vs. shared by [platypus + reptiles/birds]. Is the second greater than the first? I don't know that it is, but that is what Richard is betting will be.
    adaptivecomplexity
    If we limit the comparison to genes (the data for this is most accessible), the answer is that the number of orthologous genes groups is about the same: [eutherians+reptiles/birds] = 138, [platypus + reptiles/birds] = 132.

    If you look at synonymous substitutions, the rate for humans vs chicken is 1.642, while the rate for platypus vs. chicken is 1.707. (Human v. platypus is 1.406)

    I'd have to dig a little more for data on other genomic elements, but the results will probably be about the same: if anything, humans are more similar to reptiles in these comparisons, but really both seem to be about equally similar to reptiles.

    Mike

    Mike
    T Ryan Gregory
    As I thought, but thanks for digging through the paper!
    That was a hurried post this morning as our working week has started here (in New Zealand). I am not sure how exactly to interpret that data, I will give it some thought this weekend, but I think the bet is still on – with clarifications.

    This is what I am saying: 1. The platypus is more primitive than us. Definition of primitive – more similar genetically to our common ancestor than us. Why do I say that? Because you tell me previously all mammals laid eggs. This was an ancient trait which the platypus has retained, but not us. The platypus is a monotreme. I am assuming that this is also an ancient trait? The platypus has retained that - not us. The platypus has derived many traits since, but since it has held onto, at least, two ancient traits and the genes that derive these traits, I am betting there will be more. Also we have branched into many many species, acquiring new genes and shedding old ones in the journey. The platypus line in contrast is pretty thin. This also leads me to suspect that it has hung onto many more ancient genes than we have (not evolved as much as we have).

    2. The platypus is "genetically more closely related" to reptiles (and birds?) than us. This again requires a definition of genetic relatedness. As you said, during the course of our separate evolution we have retained, lost and gained many genes. Modern Reptiles have also gained and lost many genes from the ancient common ancestor of reptiles and mammals. But they have remained reptiles, whereas we have become mammals and further homo sapiens. This leads me to suspect that they have retained more of the ancient reptilian genes than we have.

    Putting the two together the platypus should have more common genes with modern reptiles. Again since there are many modern reptiles and birds some will be more closely genetically related to their ancient ancestor than others (having retained more of their original genes). Obviously because of the common ancestry of all life we are looking for subtle differences.

    But the genes we are concerned with are those derived from the original ancient genes and not newly acquired ones. As you have pointed out the venomous genes between platypus and snakes are not due to any common ancestral genes.

    T Ryan Gregory
    I discuss a number of these points in my paper, including "long branch equals no change" and "basal equals primitive", both of which are at the heart of your argument. You're assuming the following: 1) That one particular trait (egg-laying) is more indicative of "primitive" status of the entire lineage than other traits (e.g., venom). But "primitive" is specific to traits, not whole lineages. The platypus is highly derived in many characteristics, though it happens to retain egg laying. A whale could argue that humans are primitive because they still live on land, have four limbs, no blowhole, no echolocation, etc. You can't choose one character and consider the entire organism primitive based on that one feature. 2) That genetic change only occurs at speciation. Speciation does involve changes, but lineages can also undergo considerable genetic and morphological changes without becoming highly diverse. Hominids are a great example of this -- lots of change, but low species diversity.
    Thank you, that is pretty much what I was trying to get across with my comment about "value judgments."

    When we say that platypi are primitive because they lay eggs and have mammary slits instead of teats, which are probably features that they share with our common mammalian ancestors, we're making a value judgment. We're more advanced, because we don't lay eggs like the ancient mammals. We're different!

    But platypi are different too. They have the venomous barbs and the electrolocation. We "advanced" mammals still use our eyes and ears and noses to find food, like our 160-million-year-old ancestors did, but the platypi evolved a better way. We still defend ourselves with claws and teeth and blunt-force trauma (or, some of the more enterprising of us actually use tools), while the platypus evolved poison for that.

    When it comes down to it, there's no such thing as "more advanced" and "less advanced"--that is, in and of itself, a value judgment. Every species is perfectly adapted to exist within its particular evolutionary niche. And if the platypus had any evolutionary pressure to evolve away from egg-laying, it probably would have. But apparently egg-laying has been working out for it for 160 million years, so why change now?

    Just as well to say humans are bird-like because both humans and birds breathe oxygen and have two eyes.

    adaptivecomplexity
    This leads me to suspect that they have retained more of the ancient reptilian genes than we have.

    They haven't - that's what the orthologous gene comparison says.

    There are 132 'orthologous groups' in the platypus and chicken genomes, but not in other mammals. These are sets of genes that are most likely the 'original' ancestral genes (although they have of course changed over 300 million years) that have been retained by the platypus and modern reptiles, but not retained by us.

    When you look to see which probable ancestral genes we (eutherian mammals) share with reptiles/birds (represented by the chicken genome), which are not in the platypus, the number is 138 orthologous groups. Thus we have actually retained more ancestral sets of genes than the platypus has - we share more with reptiles, but really, these numbers (132, 138) are similar.

    If you look at orthlogous groups present in the chicken genome, and all mammals except the platypus, that is marsupials and eutherians together now, you find that there are 1526 groups that have been lost in the platypus but retained by all the other amniote lineages. You get the same result when you look at individual genes, instead of orthologous groups: 82% of platypus protein-coding genes have orthologs in all mammals and reptiles, whereas 86% of human protein-coding genes have orthologs in all mammals and reptiles.

    In each case, the comparisons suggest that if anything, we are genetically more similar to reptiles than the platypus is.

    Keep in mind that we talk about comparing sets of genes - orthologous groups, because it's difficult to make exact 1:1 comparisons. One genome may have multiple copies of a gene, while there only may be a single copy of the corresponding gene in the other genome. That's why we talk about orthologous groups.

    Mike

    Mike
    OK so apparently I was wrong in making the assumption that platypus retained more ancestral genes than humans. It was a reasonable hypothesis but not borne out (so far) by the evidence. I wonder what was meant by "reptile-like" and "bird-like" genes. Was this just a "careless use" of language?

    Thanks for the links to your paper. Obviously it will take a bit of reading which will have to await the weekend – but just a few quick thoughts. I agree that we cannot pick one trait and assume primitiveness on that basis. But assuming two species have diverged from a common ancestor. One species retains 10 original traits of the ancestor, whereas the other only 9. Would not the organism that has retained the larger amount of the original traits be more "primitive" than the other? In determining relatedness I suppose all traits should be considered exactly equivalent to each other? - Unless there was an objective scientific way to grade the importance of traits.

    Ancestral traits should determine relatedness and not derived ones, such as the venom in the platypus.

    From other aspects all traits are not equivalent. The evolution of our brain is obviously an important part of what makes us human and is more important from that aspect than the evolution of our ears or nose.

    The whale could argue, if the whale could argue, but instead we have to argue on behalf of the whale. (Maybe the whale and dolphin can argue but we don’t know if they can). Usefulness is also a criteria in evolution. The horse and the antelope retained their four limbs to get away from their predators and we freed up two of our limbs from locomotion and used them to build tools. The whale and the dolphin have highly developed brains but are severely handicapped in that respect, as we would be if our arms suddenly dropped off. The only creatures that could build an aquatic civilisation would be the octopus, though their brains I believe are not nearly as developed as dolphins, but getting there - but I digress.

    Genetic changes do occur without speciation. But it is also true that many creatures have remained relatively unchanged for millions of years (the crocodile perhaps?). Also occasionally living fossils like the coelacanth appear. Would they not be considered "more primitive". If we were suddenly to come across one of our ancestral lines living in an equatorial forest that line would be more primitive. Whereas that maybe unlikely, what maybe more likely is a species that has retained more ancestral genes than a sister species and could thus could be on that basis be considered "more primitive"?

    T Ryan Gregory
    As noted, "primitive" or "derived" refers to characters, not organisms. You could say that one species exhibits more primitive characters than another, sure, but it's still character-by-character and depends on which ones you compare. Living fossils may be unchanged in many physical regards, but not necessarily in molecular terms. And they need not resemble the ancestor shared by any living lineages. We have a tendency to make a big deal out of characteristics that make us unique, but there is not necessarily an objective reason for doing so.
    "Living fossils may be unchanged in many physical regards, but not necessarily in molecular terms"?? – When you say "not necessarily" do you accept that they may be also relatively unchanged in molecular terms? Or are you inclined to believe that they would invariably be greatly changed in molecular terms though virtually unchanged morphologically? Is there quite some evidence to support this view? Are you making this statement on the basis of the study of the tuatara?

    Whereas I would agree with that good kiwi, Allan Wilson, that the rate of molecular evolution need not move in lock-step with morphological evolution, and there is no good reason why it should, to believe that the tuatara, which has remained virtually unchanged morphologically for 140 million years, should be the fastest evolving creature strains the credibility somewhat. Add to that the fact that the tuatara is slow growing and slow breeding makes it even more incredible.

    Morphological changes such as the limbs of the whale dropping off, it developing blow holes and its body becoming fish-like are in response to environmental pressures, as would be the Giraffes long neck, birds beaks etc. etc.

    Could the fact, that the tuatara remained (morphologically) unchanged for 140 million years, not be due to the fact that it lived in an isolated environment that was in ecological balance for 140 million years and thus was not subject to evolutionary pressures like the giraffe or the whale or hominids or homo-sapiens for that matter?

    This morphological stability also implies stability of the genes that support its structure and internal organs (and even immune system to a large extent? - in the absence of new challenges to it.).

    When that isolation was breeched and the ecological balance upset, by man 1000 - 800 years ago, the tuatara was virtually wiped out in the main islands of New Zealand - it now clings on precariously on a few rocky hard to reach islands - it may then have scrambled to evolve under severe ecological stress – a case of too little too late?

    Does molecular evolution move at a steady pace like clockwork for some reason? Or is it punctuated and moves in a jerky fashion in response to environmental challenges or stress? Surely any evolution if it is a result of a chance mutation, that actually works rather than being harmful, would move in such a jerky fashion?

    If the tuatara evolved at the same pace as has been measured recently, over its entire 140 million years of existence, surely it would have evolved beyond recognition by now? On the other hand if the hypothesis that this molecular evolution is a very recent happenstance (by chance or whatever other reason) then the molecular evolutionary curve would not be a straight line and, if my hypothesis is correct would curve upwards in recent times, when plotted over time.

    I believe that the samples of DNA collected were over a period of 8,000 years from the present. Are there sufficient amount of samples for an accurate analysis? It would be interesting to look at the data.

    The Coelacanth and other fish in the ocean may also have survived by living in oceanic "ecological islands". Just a thought.

    Assuming that you do not agree with my "hypothesis" on the evolution of the tuatara, what other explanation could you offer for its (apparently) rapid molecular evolution and its failure despite that to morph into anything else, except a remarkably similar reptile to what it was 140 million years ago?

    T Ryan Gregory
    As I keep saying, it depends on what character you examine. Most of the genome is non-coding and much of it can evolve neutrally (or nearly so), regardless of morphological considerations. Some genes will evolve quickly in one lineage whether it has some primitive traits or not, because all modern species also have derived characteristics. Don't get me started on the tuatara story -- the press on that one was almost as silly as with the platypus.
    Mike, you are so tolerent of the questions people ask who just don't really get it about platypuses, genes, mammalian relatedness, bla, bla. You deserve something humorous and fun to break up the monotony and lack of elastic thinking going on with certain annoying, repeating comments.

    How about my quote of a new age "expert". Should really give you a hearty chuckle!
    The Inner Truth Adventures of
    Shushi La-La*, Vibratory Empowerment Expert:
    (* A spiritual healer whose name was channeled from the ancient Atlantian and means “Dance of the Happy Fish”)
    Shushi La-La will now speak on the power of THE GREAT MOTHER PLATYPUS

    OK students of the Great Mystery!— it’s time to shake out your chakras, swing your hips, and raise your mojo bag high, because Spring is coming and the Gluteus of The Great Mystery is Maximus!
    OOOOOOOOooooAAAAaaahhhhhUUUuuummmEEEEEEEeeeeeeei i i i i i Yi Yi Yi Yi Yi!! HUA! Hæ!
    Oh Baby! Doesn’t it feel good to get that out?

    At this equinox time of balance, we honor the GREAT MOTHER PLATYPUS of existence. She who has both MILK and EGGS to give; as the universe has both STAR-path and EARTH-path to tread upon with the Birkenstocks of the soul. Repeat with me, oh students of the divine—Oh Great Mother—MO THERE…Mo there than we can fathom…Ahummmm….MOT-HER…Great Divine name of MOT that is HER…Ahummmm…MOTH-ER, Moth of the great ancient temple of ER, symbol of fruitfulness that flies into the flame of our BEING….Ahummmmm…Oh be with us at this time of spring floods! Of floods that wash away our inequities! Of water that mixes with the dry dirt of our apathy! Of rains that beat against the dust of our mediocrity! Of rivers that flow with the mud of a new age with better credit cards! …Ahummmmm. Oh form us with your Platyputian tail of mud-hurling perfection! Ahummmmm!

    Yes, the Great Mother Platypus is a symbol of spring, and has much in common with the Easter Bunny, but first I must digress into some background history.

    The image of the Great Platypus as the divine mother of creation was first used by stone-age humans to plaster the kitchen area of their cave walls. Much the same way modern people use wallpaper of geese with blue bows on their necks to decorate modern kitchens. The platypus produces both eggs and milk, and so all smart cave people wanted a few to keep around for a handy food source, although it’s not easy milking an angry, slippery platypus. The platypus soon became an indispensible resource, and ancient humans brought platypuses with them as they spread around the world. They were revered as symbols of feminine fertility and grace, and the term “Pussy” was first used to describe the remarkably slippery, furry, fertile platypus. Pussyjuice, as platypus milk was called, was drunk by everyone—although it does have a faint scent of fish, due to the platypus’ aquatic diet. Platypus eggs were known as eggs-pussy, and were a rare treat since platypuses lay them only in the spring. Eventually, pussy became a term used to describe particularly juicy parts of human female anatomy, and eggs-pussy became ecstasy—a term for the excitement possible when exploring that anatomy.

    Unfortunately, at the end of the last ice age, there was a great amount of flooding that caused many beloved platypuses to wash away. As the platypus is a semi-aquatic mammal, it could not resist swimming away in the torrents of water flowing everywhere. When the rains stopped, the platypuses were left high and dry, and soon desiccated and died. Deprived of their staple drink of pussyjuice, humans soon attempted domesticating cows for their milk. Cows, being much heavier than platypuses, also had the added benefit of not easily washing away in floods. Eventually, people forgot about the Great Mother Platypus and her gifts of eggs and milk. But the term “pussy” remained, and an ecstatic spring rite that honored eggs-pussy was still being celebrated every equinox—called “Eggster”. This eventually became Easter which was a holy day long before the birth of Jesus.

    The Easter Bunny myth first started with Christian monks of the 11th century who wanted to blend Christianity with the popular Pagan fertility rite of the chocolate testicle-toss off. As the monks knew that church officials would not endorse anything to do with chocolate testicles, they changed the image of the celebration to chocolate eggs. Happily, they discovered that eggs were as easy to dip in chocolate as testicles, if not quite as much fun.

    The image of the Easter rabbit was used by the monks as a substitute for the giant vagina tapestries the Pagan villagers would weave out of the crotch-hairs of oxen. Although bunnies are excellent fertility symbols—and just as touchably soft as oxen crotch hairs—it was difficult to get the villagers to give up their vagina tapestries. It seems the simple folk of those times liked their vaginas out in the open were they could be seen by all. The villagers believed the vagina tapestries were blessing their fields with fertility every time they flapped in the wind. Once those clever monks caught on they came up with a substitute for flapping vaginas as fertility symbols—the idea of bunnies hiding the eggs in the fields and then the villagers gathering the eggs with a basket to “capture the fertility”. While not nearly as colorful as huge vagina tapestries, baskets full of eggs became the official Easter symbolism.

    So you see, the wisdom of the Great Mother Platypus is hidden beneath the joyous egg-hunting of Easter. Let us all raise our voices in celebration of THE GREAT PUSSY! The pussy from which all eggs are hatched! The Pussy who’s milk is overflowing! The PUSSY who is and was and always will be! Hail wondrous, wet, furry,
    PLATYPUUUUU-SSSSSSSsssssssss-YYYY!!!

    adaptivecomplexity
    That's hilarious.  A little, uh, shocking, but hilarious.
    Mike
    Dear Mike: Sorry to be shockingly uncensored in the, um...creatively enhanced version of platypus history.
    You see, I wanted to be a scientist when I "grew up", but my inherently wacky nature got in the way. So I went for the "inner version" of science--art and creative writing!
    I have however, aborbed ridiculous amounts of mostly useless scentific trivia about things such as creeping slime molds and snail sex during my years of scentific yearnings. So what is a sleep-deprived human with secret scentific yearnings and creative impulses to do? Is there a stand-up comedy venue for scientific types?
    I wouldn't take up space on your site with my nonsense--except, well, look at some of the replies you get--boy, are some folks just plain dumb--and boringly dumb. At least I'm entertaining.

    If any dumbos are reading this--Of course platypuses are mammals! Have you looked under your shirt lately? Nipples. Mammals--mammary glands--get it stupid? Platypuses have milk--they are not reptiles anymore than stupid humans are throwbacks. Yes platypuses lay eggs--so what? I've seen men with hair on their backs that would make a gorilla jealous--does that mean men are "more primative" than women? Should we lock up hairy men in zoos for display to the less hairy? What superiority complexes some of these quasi-scientific folks have! They want to believe everything is "below" us on the evolutionary ladder. "My brain is biggest!" They whine. "So that makes ME the best because I say so!" HA HA! How do you keep from telling people that their arguments are devoid of logic and a waste of the big brain they think is Soooo fabulous?

    T Ryan Gregory
    I think you are still confusing similarity with relatedness. Relatedness refers to who is descended from whom. You are not any more closely related to a brother than to a sister, though you share some genes with a brother (the Y-linked genes) that you don't share with a sister.
    On the contrary - relatedness needs to be redefined on the basis of genetics.

    Even among siblings if I share more genes with one sibling than another then I am more related to that sibling than the other. Identical twins are more related to each other than their other siblings.

    The same would apply - and indeed be greatly magnified over time in the divergence of species

    T Ryan Gregory
    I see what you are trying to argue, and I am not disagreeing that in some regards, both physical and genetic, platypus is less derived than placental mammals. However, phylogenetically they are not more closely related to birds than humans are. They may, however, be more similar in some genetic regions and not others, just as they may be more similar physically in some features and not others. The common ancestor was not a platypus, nor a bird, nor a snake, nor a lizard, nor a crocodile. All of these have changed considerably since they have diverged. The point of this post is that a modern species is not a mixture of traits of other modern species. The point of my discussions is that one cannot assume that any given feature of a platypus is more like the ancestor simply because they are more "basal" phylogenetically, because modern species that share a common ancestor are equally related (though obviously not necessarily equally similar) to other types of organisms that do not share the ancestor.
    OK I can agree with that

    Hank
    It's not just the platypus getting shorted by the mainstream media. Sloppy brain evolution is getting blamed for dumb things people do too.(*)

    Our attempts to pursue our goals are often thwarted by the fact that evolution has built our most sophisticated technologies on top of older technologies -- without working out how to integrate the two.

    I hope I don't secretly have venom in my toes.

    Hank

    (*)Not me. In the ### below the article, professor Marcus clarifies that I rule.

    Thanks for the intellectual insight- something you won't find on an american television or radio or lamestream media website except by pure accident.

    I'm wondering if you can speak to the concept that humans have the gene to have fur- it's just mega recessive.
    http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=318436

    Examples in human history used to be either thought of as bigfoot or travelled with a circus as a lion man, etc...

    Thanks for sharing such an informative article with us. The platypus…has been known for a long time to have a very curious amalgam of anatomical features. So the interesting question is when we get a look at its DNA would it also have a curious amalgam of genetic features…it sure does. In fact, parts of it apparently were extremely difficult to sequence because they were so different from other mammalian genomes, to which we often compare sequences in order to align them and put the sequence together. It has not just a curious combination of mammalian and reptilian physiological features, it has a curious combination of mammalian and reptilian genetic features as well.