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    Platypus Sex Chromosomes And Basal-Equals-Primitive
    By T. Ryan Gregory | May 9th 2008 11:17 AM | 8 comments | Print | E-mail | Track Comments
    About T. Ryan

    I am an evolutionary biologist specializing in genome size evolution at the University of Guelph in Guelph, Ontario, Canada. Be sure to visit

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    There has been considerable interest in the publication of the platypus genome, which is good. Unfortunately, much of the reporting has been distorted, which is bad. However, rather than picking on the press, I want to focus on an example from the scientific literature where a misconception about evolutionary relationships seems to creep in and generate confusion. Consider the following line, from a soon to be published paper about platypus sex chromosomes (Veyrunes et al. 2008).

    As the most basal mammal group, the egg-laying monotremes are ideal for determining how the therian XY system evolved.

    Now, the study's conclusions are interesting. While most mammals show an XY system (males XY, females XX), the monotreme system is quite unique (5X5Y males, 5X5X females), and has some similarities to birds in terms of which genes are involved in determining sex. Thus, because monotremes have a system quite different from therians (placental and marsupial mammals) and the split between monotremes and therians occurred earlier than that between placentals and marsupials, the system in therians must have evolved after the split between theirs and the monotreme lineage. Also, one can identify regions on platypus autosomes that correspond to the sex chromosomes in other mammals, suggesting that the therian sex determining genes are derived from former autosomal regions (this was already apparent through comparisons with other non-mammalian vertebrates).

    The problem is the way this is framed. The platypus is a modern species. Like all modern species, it retains some ancestral characters (e.g., egg-laying and milk secretion without nipples), posseses many highly derived characters (e.g., electroreception and venom), and shows convergent evolution with some other groups (e.g., "duck bill"). It is entirely possible that the chromosomal system in platypus is similar to the one found in the common mammalian ancestor, but to assume that because this species is "basal" (i.e., "early branching") it must be primitive in terms of any particular characteristic is a fallacy that I have mentioned previously (Phylogenetic Fallacies: Early Branching Must Mean Primitive; see Crisp and Cook 2005; Gregory 2008).

    Imagine if a paper said something like

    As the most basal mammal group, the duck-billed platypus is ideal for determining how the therian feeding system evolved.

    One's immediate reaction would be, "But the ancestral mammals did not have anything like a 'duck bill'!".

    Another issue arises when the authors (and especially the press) say things such as,

    Monotremes ... display a fascinating mixture of mammalian and avian/reptilian morphological, physiological, and karyological features..."

    Monotremes do not possess bird characteristics. Either monotremes and birds demonstrate convergence, or exhibit co-option of the same features in a superficially similar character, or both retain a feature that existed in a common amniote ancestor which may have been lost in other mammals and/or modern reptiles. The comparisons are being drawn between platypus and bird (chicken) genomes in recent studies largely because there are no reptile genome sequences yet available, and because phylogenetically birds are reptiles, though very derived ones. Because we share a common ancestor with monotremes that is not shared with birds, humans and platypus are equally closely related to birds. Using the same logic found in many news stories, one could argue (falsely) that humans are more bird-like than platypus because we are bipedal, for example. When a paper states that a platypus feature, such as its sex chromosome content, is "bird-like" or "derived from an ancestral bird-like system", they are not saying that it is actually derived from a bird. One also could just as easily say that birds have platypus-like chromosomes, though this would be more awkward because the bird system was understood first and because there are far more birds than platypus (10,000 species to 1) -- but it is not because platypus is primitive and birds are "advanced". In fact, under the hypothesis presented by Veyrunes et al. (2008), birds have sex chromosomes more similar to the ancestral amniote system, making them more primitive than the platypus.

    Finally, the authors present a phylogeny with -- predictably -- humans at the top and increasingly un-human-like groups branching off at earlier and earlier dates. As noted in an earlier post [Phylogenetic Fallacies: Branching From a Main Line], each node can rotate without affecting tree topology, such that this neat story is not so tidy. Here is the tree they presented (redrawn in simpler form).

    Here is an equal tree in terms of relationships.

    The same hypothesis regarding chromosomal evolution (a primitive bird-like ZW system, modified only slightly in modern birds, more in platypus, and replaced with a very different mechanism in other mammals) could fit the second tree, but it would not be as obvious.

    The main point is that comparisons involving platypus, opossum, humans, rodents, birds, and other vertebrates are interesting and informative, but one must not forget that these are all modern species whose lineages have been evolving for exactly the same period of time since diverging from a common ancestor. None as a group is "primitive", rather some retain more specific ancestral characteristics than others, but all are highly derived with regard to other features. This applies to the genome as well as to fur, feathers, and bills.

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    For more on this topic, have a look at Nimravid, Adaptive Complexity, and Pharyngula.

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    Crisp, M.D. and L.G. Cook. 2005. Do early branching lineages signify ancestral traits? Trends in Ecology and Evolution 20: 122-128.

    Gregory, T.R. 2008. Understanding evolutionary trees. Evolution: Education and Outreach 1: 121-137.

    Veyrunes, F., P.D. Waters, P. Miethke, W. Rens, D. McMillan, A.E. Alsop, F. Grutzner, J.E. Deakin, C.M. Whittington, K. Schatzkamer, C.L. Kremitzki, T. Graves, M.A. Ferguson-Smith, W. Warren, J.A. Marshall Graves. 2008. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Research, in press.

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    Comments

    adaptivecomplexity
    It's too bad the Nature paper itself has these problems. But genome sequencing consortiums have never been especially good at getting this kind of thing right. Exhibit A is the claim of widespread bacterial horizontal transfer made by the authors of the Human Genome draft sequence paper, a mistake which could have been avoided by checking with the evolutionary biology community.

    Mike

    Mike
    I'm curious what people think about still using the traditional way of ordering phylogenetic trees of mammals, with humans at the top. I find it convenient to see trees in that approximate order because it makes it a little easier to visually compare between trees from different studies. For that reason I almost always put humans at the top.

    In my own analysis I try to maintain as consistent an ordering of taxa as possible because that makes the differences between trees stand out much more clearly. I do understand and agree that not putting humans at the top might do a lot to dispel the ladder of evolution notion that most people have, but I do appreciate the ease of comparison that comes from ordering species in typical humans at the top branching from a main line order.

    Any opinions?

    Arjun

    Wait they have 10 sex chromosomes? Are all the Y's and X's tied together somehow?
    Why don't you find yourself seeing all sorts of polygenic-inheritance type sex chromosome ratios, like 6x-4y?

    T Ryan Gregory
    From the article:
    The male was discovered to have 10 unpaired chromosomes that included five male-specific Y chromosomes and five X chromosomes; the female possesses two copies of the five Xs. In male meiosis, the 10 sex chromosomes form analternating XY chain, X1Y1X2Y2X3 Y3X4Y4X5Y5, unique in vertebrates. These 10 chromosomes pair and recombine in pseudoautosomal regions at the termini of adjacent X and Y chromosomes.
    In fact, under the hypothesis presented by Veyrunes et al. (2008), birds have sex chromosomes more similar to the ancestral amniote system, making them more primitive than the platypus.

    Are you saying you actually believe everything in that paper? It doesn't even make sense to propose the avian sex chromosomes as ancestral to the reptilian lineages, let alone all amniotes -- just look at Figure 4 of that paper again, and see if you can explain how the authors reach their conclusions.

    There's actually not a lot of overwhelming synteny between the platypus sex chromosomes and the chicken Z. I suggest looking at the primary data, the actual genome sequences, not the FISH results obviously cherry-picked by Veyrunes et al. Point your browser to UCSC Genome Browser load up the chicken Z and turn the platypus and human synteny tracks on. You'll see something interesting, I promise.

    Just because something gets published, doesn't mean its correct -- another point the Veyrunes et al. paper makes nicely. The paper essentially exists to correct nearly 2 decades of erroneous results from the senior author's lab. Read it a little more closely.

    T Ryan Gregory
    Are you kidding me? You got from my post that I uncritically accept their interpretation? My quote above refers to the fact that their hypothesis birds would be more "primitive" than platypus, which is relevant because my point was to critique their phylogenetic assumption.
    As more efficient sequencing techniques advance, more genomes come to light. The Platypus genome is still and most likely will be one of the strangest animals ever studied which man continues to be perplexed by, but one's thing is for sure, it's an interesting topic to discuss.

    I agree, not all what is published should considered facts which are infallible.

    The biology of the platypus, like the biology of every living species, cannot be fully understood unless the process of life is underetood. DNA is present in every living species and is an organic molecule that is respondent to the affects of its environment. The environmental affects are always in the form of pulsating energy when they access the DNA molecules causing vibration of the nucleotides with physical and electro signalling results. The physical effects, of a changed environment, if severe enough in prolonged application and/ or severity cause permanent strain (or records) invoking corrective actions when the specimen reproducess (Evolution of genes and DNA memory) Evolution of the species occurs when the evolved genes etc are passed on by the process of inheritance, adapting the species to survive in the changed environment. The electro signalling effects (switching) of the genes regulatory memory activate the genes to control the physical day to day survival requirements, whilst the effect on the DNA devoted to mental control is to activate thinking capacity and conscious memory . Understanding this process allows causes of cancer, dementia. diabetes etc to be established and how the sexual characteristics of the platypus etc evolved. For further discussion refer to my homepage http://evolgenmutsuic.com and for further papers "Life and Evolution" (What life is and how it responds to and is driven by the energy effects of its environment) and "Epigenetics" (How the required output from specific genes and DNA is accessed and controlled) and other papers please indicate interest to John, at pabudgie@aol.com