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Tuesday, July 12, 2011

Can Somebody Please Translate This?

Denise O'Leary has discovered a paper that was written up in Science News Daily: Chromosomes' Big Picture: Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place. She seems to think this causes a problem for evolution.

I couldn't make head nor tail of the posting on Uncommon Descent [Most life forms show S pattern in chromosome lengths, guess which one doesn’t?] but that didn't surprise me because, after all, it was written by an IDiot. However, I was a bit surprised by the Science News report because I couldn't understand it either.

So I looked at the original paper. Here's the reference and abstract.
Li, X., Zhu, C., Lin, Z., Wu, Y., Zhang, D., Bai, G., Song, W., Ma, J., Muehlbauer, G.J., Scanlon, M.J., Zhang, M., and Yu, J. (2011) Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary. Mol. Biol. Evol. 28: 1901-1911. [doi: 10.1093/molbev/msr011]


Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organisms. Although the genome of a species as a whole is important, chromosomes are the basic units subjected to genetic events that coin evolution to a large extent. Now many complete genome sequences are available, we can address evolution and variation of individual chromosomes across species. For example, “How are the repeat and nonrepeat proportions of genetic codes distributed among different chromosomes in a multichromosome species?” “Is there a general rule behind the intuitive observation that chromosome lengths tend to be similar in a species, and if so, can we generalize any findings in chromosome content and size across different taxonomic groups?” Here, we show that chromosomes within a species do not show dramatic fluctuation in their content of mobile genetic elements as the proliferation of these elements increases from unicellular eukaryotes to vertebrates. Furthermore, we demonstrate that, notwithstanding the remarkable plasticity, there is an upper limit to chromosome-size variation in diploid eukaryotes with linear chromosomes. Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes (including 22 human autosomes) can be viably captured by a single model, which predicts that the vast majority of the chromosomes in a species are expected to have a base pair length between 0.4035 and 1.8626 times the average chromosome length. This conserved boundary of chromosome-size variation, which prevails across a wide taxonomic range with few exceptions, indicates that cellular, molecular, and evolutionary mechanisms, possibly together, confine the chromosome lengths around a species-specific average chromosome length.
Here's the challenge. Read the abstract and try and guess what important scientific point the authors are making that deserves publication in a molecular evolution journal. For extra points, read the entire article and see if you can improve your guess. You'll be impressed when you read the discussion and it all becomes clear (not!)


  1. That's not Science News, that's Science Daily, the press-release regurgitation site. ("Science News" is their label for the type of content.) Big difference.

    What you are looking at is a a release from the university press office, so if it's incomprehensible it's their problem.

  2. The authors seem to be saying "Chromosome sizes follow a normal distribution, except it's truncated at the ends and there are some outliers like birds and platypi." Or am I missing something (I did an extremely brief skim).

    Mildly interesting. National news? Not sure. There are quite a few things in the world that roughly follow a normal distribution...

  3. Sorry, I fixed it to Science Daily but I wasn't under any illusions about the ultimate source. University press offices are notoriously bad.

  4. 1) Chromosome size seems to be broadly similar within any given organism if we squint a bit - can we find a mathematical distribution that encapsulates this?

    2) Yes

    3) Except for birds, reptiles and amphibians, which quite happily exist with microchromosomes and macrochromosomes varying in size over more than three orders of magnitude.

    4) But we didn't analyse any of those, so we're cool.

  5. the idea that platypuses share some uniquely specific molecular characters with birds is a persistent myth. The original paper on the platypus genome had a chicken as the only representative of the sauropsids (i.e., the reptile/bird clade of the amniotes).

    The genetic features that platypuses share with bird are generalized amniote features that have been lost in more derived (therian) mammals. One obvious morphological primitive amniote feature retained in both monotremes and birds is egg laying --- but others exist, such as the retention of the coracoid bone in the shoulder girdle.

    And, of course, all mammals share features (genetic and morphological) with reptiles, amphibians, fish, etc. To make it appear as if the platypus is somehow a unique chimera here is pandering to absurdity.

  6. Hi, Larry! There's a second occurrence of "Daily News" further down.

    I get:

    * Chromosomes in a genome have a similar number of mobile genetic elements, whatever those are.

    * Autosomal chromosomes in multi-chromosome species are generally the same size within a factor of about two.

    Discussion: This may be because it makes the duration needed to synthesize each chromosome similar or for some other reason.

    How am I doing?

  7. I haven't actually done anything so extreme as reading the original paper but ... there has been a lot of past work on variation of karyotypes including using null-models that just have random rearrangements and finding pretty good fits. I recall work back in the 1970s by Imai, Takeo Maruyama and Ross Crozier (in American Naturalist). I am assuming this is also carefully discussed in Mike Lynch's recent major book.

    So do these authors cite all that past work? I hope so. Also how do they make the muntjak deer fit? It has all its genes in just three pairs of chromosomes, which makes them a bit bigger than our chromosomes, I would think! Or what about the ant Ross Crozier found (Myrmecia pilosula) which has one pair of chromosomes -- and in males which are haploid just one chromosome. Wonder how well that fits on that S-curve?

  8. I looked at the paper, which is an exercise in curve-fitting with data from many species. It's not totally silly. And it doesn't say that absolute chromosome sizes are constrained (as I had thought) but just relative sizes. But chickens and the one-chromosome ant Myrmecia would seem hard to fit with that theory. They do cite one paper by Imai, and Mike Lynch's book.

    The paper is Open Access so everyone can take a look.

  9. @Joe Felsenstein,

    I was thinking about posting something on the Indian and Reeves muntjacs but I've been pretty busy finishing off my book.

    The one chromosome in Myrmecia is also an interesting fact when thinking about karyotypes.

    Having read the paper (twice) I'm still not sure what the point it. It's nice that they reference Mike Lynch but what does it mean?

    Can you give me a one or two sentence summary of their main conclusions?

  10. Larry -- they do a lot of curve fitting on sizes of chromosomes, conclude that variation of chromosome size fits having a reasonably constant coefficient of variation (standard deviation as a fraction of the mean), and from that they suggest that there is selection against having too high a variation in chromosome size among different chromosomes within a species. How this fits with chickens and their microchromosomes I do not know.

  11. Here's a part of the abstract of a paper I am working on for "Journal of Self-evident and Recursive Results" (revise and resubmit). I think it timely considering that this paper is now on the scene:

    "Now that digital tape measure technology has become accurate to the nanometer scale, we investigated human heights from a range of subpopulations. Here, we show that the presence of mobile foot protectors does not have a strong influence on our measurements. Strikingly, one model seems to fit all of our results: it predicts that all human heights are within .26 and 1.82 times the average measurement, unless the measurement is an outlier, all of which were removed prior to analysis. This upper bound suggests that there is a profound evolutionary pressure, a scale naturae if you will, that limits human height to the upper bound. Finally, we ponder the general increase in body length from invertebrates to humans".

    I am a generally for the computational/statistical exploration of biological data, but if anyone has read the book Proofiness (which I recommend), you will recognize that this type of curve fitting exercise would serve as a prime example of Rorshach's Demon. I confess that I haven't read the entire paper for details, but the satire above characterizes the impression I get from the abstract.

  12. I'll have a go of it. How about spanish: La comprensión del genoma y la evolución cromosómica es importante para comprender la herencia genética y evolución.

    sorry, couldn't resist

  13. There is no doubt about it. The platypus is a real enigma, just like the red panda. It has reptilian, mammalian and avian features and this is reflected in its sex chromosomes. Of course, with HGT anything is possible for evolution!

  14. @atheioclast

    I see that someone didn't read my previous post, which started thus:

    "The idea that platypuses share some uniquely specific molecular characters with birds is a persistent myth. The original paper on the platypus genome had a chicken as the only representative of the sauropsids (i.e., the reptile/bird clade of the amniotes)."

    The red panda is hardly an enigma -- it's classified in its own family "Ailuridae" within the arctoid carnivores, although there is still some controversy about how the various non-canid arctoid families are interrelated.

    BTW, assuming that you are human, you also share many features with reptiles and birds, to the exclusion of other vertebrates. Those would include a trachea, a metanephric kidney drained by a ureter, an archinephric duct (now = vas deferens) that drains only the testis (assuming that you are male), a pterygoideus muscle as one of your jaw closing muscles, a lagena (= cochlea) for hearing, etc. etc. Are we feeling enigmatic enough yet?

  15. Not a comment to this thread, really, but a question that arises from Carl Zimmer's blog, The Loom, and a short post Goodby E Coli. What is a species particularly in reference to bacteria, which of course are not sexual, although they can trade DNA from one to another by various means. Does species not generally refer to sexual organisms? Since bacteria do not require any trading of DNA in order to reproduce is not each bacterium essentially its own "type" so to speak?

  16. I wish I could say that that was the most convoluted abstract I have read. But, alas, it is not. Shudder while you imagine worse, he, he, he!

  17. Most eukaryotes have chromosomes whose sizes are within five-fold of each other.

    Probably because the mechanics of cell division do not work well if the chromosomes differ by more than this.

    Ho hum...

    It must take a lot of self-deception to describe these results as 'amazing'.

  18. The paper shows a gamma distribution of species. Extra long chromosomes can lead to mitotic instability and extra short chromosomes can be lost during meiosis.

  19. Bozogomer writes:

    "It (platypus) has ...avian features and this is reflected in its sex chromosomes."

    Let me guess - its duck bill?