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Fossils are cool, but some of us are interested in processes and structures that don’t fossilize well. For instance, if you want to know more about the evolution of mammalian reproduction, you’d best not pin your hopes on the discovery of a series of fossilized placentas, or fossilized mammary glands … and although a few fossilized invertebrate embryos have been discovered, their preservation relied on conditions not found inside the rotting gut cavity of dead pregnant mammals.

You’d think this would mean we’re right out of luck, but as it turns out, we have a place to turn to, a different kind of fossil. These are fossil genes, relics of our ancient past, and they are found by digging in the debris of our genomes. By comparing the sequences of genes of known function in different lineages, we can get a measure of divergence times … and in the case of some genes which have discrete functions, we can even plot the times of origin or loss of those particular functions in the organism’s history.

Here’s one example. We don’t have any fossilized placentas, but we know that there was an important transition in the mammalian lineage: we had to have shifted from producing eggs in which yolk was the primary source of embryonic nutrition to a state where the embryo acquired its nutrition from a direct interface with maternal circulation, the placenta. We modern mammals don’t need yolk at all … but could there be vestiges of yolk proteins still left buried in our genome? The answer, which you already know since I’m writing this, is yes.

First, a little background. It’s not that surprising to find traces of yolk proteins in our genomes, because we also have the evidence of embryology that shows that our embryos still make a yolk sac! Below is a series of diagrams of the human embryo over the last several weeks of the first month of pregnancy, and you can see the large sac hanging from the embryo; it’s a useless fluid filled space that contains no yolk at all, but is homologous to similar structures that form in birds and reptiles.

Sometimes people refuse to believe that we could have a yolk sac, and they don’t trust cartoons, so here’s a photo of a 28-somite stage embryo. The side view on the left nicely shows the branchial arches (they also don’t want to believe in those), but the one on the right is the same embryo rotated, so you can see the huge empty balloon of the yolk sac.

i-ddde7d1d26a9bc52cccdfd9f2de7d2cb-yolk_sac_photo.jpg

We retain the sac, but what about the contents? Where are the yolk proteins? The primary component of yolk is made from a protein called vitellogenin. Vitellogenin is a large (250-600kD) glycophospholipoprotein, which basically means that it has a protein core that is extensively modified by the addition of sugars, phosphates, and fatty acids — it’s a great greasy lump of protein, fat, and sugar, just the thing growing embryos need to eat. Animals with yolky eggs synthesize vitellogenin in their livers, and transport it the oviducts, the site of egg production, where it is deposited in the yolk sac, and also further broken down into the two major yolk proteins, phosvitin and lipovitellin. Mammals don’t make vitellogenin at all, although there are some interesting similarities between portions of vitellogenins and lipoproteins that we use to transport fats in our circulatory systems (the atherogenic lipoproteins that are the curse of our modern diets may be related to the lipoproteins our ancestors used to feed their embryos.)

We can follow the evolutionary history of the vitellogenin gene. Tetrapod ancestors, 350-400 million years ago, had two copies of the gene, called VIT1 and VITanc (multiple copies of a gene with high demand for its gene product, like yolk proteins, is advantageous for boosting output). Some time before the mammalian lineage diverged from the reptile/bird lineage, there was a duplication of VITanc to form VIT2 and VIT3 … so chickens have 3 vitellogenin genes, VIT1, VIT2, and VIT3.

How do we know that this duplication occured before the mammalian line split off? Because we also have VIT1, VIT2, and VIT3 in our genomes! They are irreparably broken and non-functional, and eroded by time, but Brawand et al. found them, and identified them by sequence similarity and by synteny, or the identity of the adjacent genes.

When non-functional genes, called pseudogenes, like this are found, one thing one can do is estimate the time of loss of function from the amount of decay. Natural selection is a force that maintains genes, and in its absence, they tend to slowly fall apart as they accumulate mutations. Browsing through the genome is like strolling through a run-down neighborhood. Houses that are still occupied will be maintained and kept up. Houses that have been recently abandoned might have an overgrown lawn and broken windows. Houses that have been neglected longer still might show signs of fire damage, or structural collapse, or might have been demolished right down to their foundations. By measuring the divergence of mammalian pseudogenes for vitellogenin from bird vitellogenin genes, for instance, we can estimate the time of loss.

Rather than counting broken windows, in genes we count the accumulation of stop codons (sequences that signal the end of transcription) and indels. An indel is a single insertion or deletion of a stretch of nucleotides in a gene, and in the lineages studied here they occur at a rate of slightly more than 1 x 10-10 per site per year, so it’s like a very slowly ticking clock that gradually scrambles the pseudogene.

The results are summarized in this diagram.

i-ed8a38419a70b0538cd921248962b01c-vit_history.jpg
(Click for larger image)

VIT Gene Evolution in Tetrapods: The topology and divergence times of the tree are based on previous studies. Latin crosses indicate VIT inactivation events in eutherians and monotremes. Inactivation estimates (including approximated 95% prediction intervals) based on opossum VIT sequences are indicated by colored bars at the top (see also Figure 3). Duplications (?x2?) are indicated. VITanc is the likely ancestor of both the amphibian vtgA1/vtgA2 and VIT2/VIT3 genes in birds. Functional VIT genes in extant species are indicated in red. The inactivation time of VIT1* on the amphibian branch could not be estimated because of its absence in Xenopus tropicalis.

The loss of vitellogenin was not abrupt. VIT1 and VIT3 became nonfunctional about 150 million years ago (note, though, the wide range of possible times, caused by uncertainty in the methods), roughly corresponding to the evolution of eutherian ancestors and after viviparity. VIT2 hung in there until about 70 million years ago, suggesting that maybe those Cretaceous mammals were still pumping a little yolk protein into those yolk sacs, as a supplemental nutrition source.

The monotremes have also lost most of their vitellogenin genes, but still retain one, to no one’s surprise — they still lay eggs. Furthermore, VIT1 was only relatively recently lost, about 50 million years ago.

One other detail in the chart is of interest. It shows that nutritive lactation arose before placentation and loss of the vitellogenin genes. Again, no one has found fossil mammary glands; instead, they looked at genes important in milk production, in particular, the casein milk genes. Casein is a secreted calcium-binding phosphoprotein that is essential for transporting calcium to the embryo, and calcium is a critical growth-limiting mineral during embryogenesis. We have caseins, of course, and the platypus is found to have orthologous casein genes, which tells us that these genes arose before the monotreme and eutherian split.

Taken together, these data tell a story. Lactation evolved first, representing a gradual shift in parental investment from storage of yolk in eggs to later, post-hatching care. This reduced selective constraints on yolk production — three genes were overkill for the level of output needed — and was permissive in allowing the gradual decay of the VIT genes. Viviparity and placentation then made the yolk proteins more and more superfluous, as embryos became more and more reliant on simply tapping directly into the maternal blood supply. The process represents a pattern of change away from stockpiling massive quantities of nutritional supplies for future growth, to a more efficient just-in-time delivery system.

The story is all right there in your genes. You’re walking around carrying the crumbling record of hundreds of millions of years of history — all we need is the tools to extract it and read it.


Brawand D, Wahli W, Kaessmann H (2008) Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol 6(3):e63.

Sadler TW (2004) Langman’s Medical Embryology, 9th ed. Lippincott Williams and Wilkins, Baltimore.

Comments

  1. #1 Bee
    March 19, 2008

    These are my favourites of your posts, though I enjoy all of ‘em. Thanks, PZed, this is fascinating. You have a genius for making biology remarkably understandable.

  2. #2 Glen Davidson
    March 19, 2008

    On Randy Moore’s movie review blog, someone lectured me about the fact that statistical analysis is a “valid branch of science” (unsurprisingly, saying it wrong).

    I thought that a bit rich from the side that denies all of the implications that statistics give us about our relatedness (according to ordinary reproductive means, by all of the evidence) to the other organisms.

    It’s so insane to think that Dembski’s metaphysical assumptions, and mathematics based on those improper claims, are taken as “statistical analysis,” when the huge amount of statistical work that gives evidence of evolutionary processes with no intervening breaks (miracles) are just ignored by these dolts.

    Glen D
    http://tinyurl.com/2kxyc7

  3. #3 Cat Faber
    March 19, 2008

    Wow. Very cool!

    Where did the embryo pictures come from? I’ve long wanted to construct a poster of embryos of various species at various stages and challenge the right-to-lifers to identify the human beings.

    After all, if a fetus is so supernaturally human it’s okay to enslave another human to preserve its life, one ought to be able to tell it at a glance from, say, a mouse or a chicken.

  4. #4 Kadath
    March 19, 2008

    Yay! ^_^

    I love geno-chronology. More posts like this one, please!

  5. #5 jfatz
    March 19, 2008

    What the hell…? Science? You still do that?

    ;-)

  6. #6 P.
    March 19, 2008

    I love, love, love these kind of posts on Pharyngula. More please!!!

  7. #7 DiscoveredJoys
    March 19, 2008

    really neat post, I shall save this for posterity.

    Curiously enough I was thinking of a possible analogy for the psuedogenes , and I got as far as ‘a reasonably maintained house with some old broken fridges and rusty cars on the front lawn’ – and then I read your neighbourhood analogy.

    That got me thinking about the relative amount of no longer useful or maintained genes – is our genotype like a house with a few rusty cars outside, or is it more like a spiffy trailer in the middle of the aeroplane graveyard in El Paso County, Texas?

  8. #8 Holbach
    March 19, 2008

    You will never convince the religious retard of this obvious evolutionary fact. It’s there because their god
    wanted it there, regardless of any prior intention or
    explanatory illustration. The freaking retards. Great stuff,PZ!

  9. #9 Wounded King
    March 19, 2008

    There is a good series of images of the Carnegie stages of human development at http://embryology.med.unsw.edu.au/wwwhuman/Stages/Stages.htm

    For mice one of the best embryonic resources is probably the Edinburgh Mouse atlas Project …

    http://genex.hgu.mrc.ac.uk/intro.html

    … which has 3 Dimensional models of various stages of mouse embryonic development. They also have a downloadable version of the original book by Theiler on the staging of mouse development.
    http://genex.hgu.mrc.ac.uk/Atlas/Theiler_book_download.html

    TTFN,

    WK

  10. #10 caynazzo
    March 19, 2008

    Great run-down neighborhood metaphor, too! Because of the shared word decay, I immediately thought of radioisotope dating as a way of understanding functional genomic decay.

  11. #11 Todd
    March 19, 2008

    Awesome.

    Now I’m curious, what pre-mammalian tissue evolved into the placenta?

  12. #12 Nentuaby
    March 19, 2008

    Thank you! I know I’ve got a weakness for pseudo-science bashing (it’s so easy and snark is fun) but it’s wondrous to see some actual positive bits about real science here.

  13. #13 Chris
    March 19, 2008

    Great post!

  14. #14 Forrest Prince
    March 19, 2008

    Dang ya, PZ, you went and made me look up “branchial arches”, and now I learned something. I hate when that happens to me.

    Gills in fishies and thyroid glands in people, both salt-regulating organs, and further evidence of the truth of biological evolution. Do I have that essentially correct?

    No wonder the fundies loathe you.

  15. #15 Shaggy Maniac
    March 19, 2008

    we count the accumulation of stop codons (sequences that signal the end of transcription)

    maybe you meant to say “signal the end of translation”?

    Cheers

  16. #16 rob
    March 19, 2008

    If this “theory” of “yolk sacks” and “evolution” is true, why don’t I see cats turning into dogs then turning into scrambled eggs?

    mmm…scrambled eggs.

  17. #17 Chris Bell
    March 19, 2008

    Browsing through the genome is like strolling through a run-down neighborhood. Houses that are still occupied will be maintained and kept up. Houses that have been recently abandoned might have an overgrown lawn and broken windows. Houses that have been neglected longer still might show signs of fire damage, or structural collapse, or might have been demolished right down to their foundations.

    That crystal clear explanation needs to be used in genetics text books post-haste.

  18. #18 Schmeer
    March 19, 2008

    I really prefer this post to thinking about parasites (did we ever come to a conclusion if they are truly parasites?) living on excreted wastes in the renal sac of a cephalopod. Then again, I’d rather think of those parasites than Ben Stein.

  19. #19 ennui
    March 19, 2008

    Yeah, but angelfood cake only has egg whites. Checkmate, atheists!

    Great post, PZ!

  20. #20 dsmvwld
    March 19, 2008

    Yeah, and we have gill slits, too, and resemble other animals while in the womb.

    Oh, no, wait. Those both have both been disproven. My bad.

  21. #21 Ian
    March 19, 2008

    So does this mean it’s fair to say that this is egg on any creationist’s face?

    Great article.

  22. #22 Michael X
    March 19, 2008

    I wonder if you can point me to the people doing the correcting dsm?

  23. #23 Dr. Moonbeam
    March 19, 2008

    Wonderfully lucid explanation… even for a non-scientist like myself.

  24. #24 Steviepinhead
    March 19, 2008

    I’ve got to also admit to a fondness for the science “articles” over some of the other genres that flourish here–though I’d miss almost any of them if they suddenly turned up missing (no Friday cephalopods–horrors!).

    And this was a great science article. I’m promptly exporting it to at least one other blog’s “cool new fossils” thread!

    Thanks, PZ.

  25. #25 Peter Ashby
    March 19, 2008

    Forrest Prince you got it right as far as you went. You can add your lower jaw, your hyoid bones and pretty much most of your throat as well as bits of your face. A lot of the muscles of the face and throat get there by the cells migrating into the arches and following along as they grow and differentiate into their final structures.

    They are also extremely useful for staging mid stage embryos, one glance will tell you how old even in mutant embryos where other bits are retarded, like the head. Been there, feel fondly about them.

  26. #26 Margaret
    March 19, 2008

    the last several weeks of the first month of pregnancy

    Should that “weeks” be “days”?

  27. #27 dsmvwld
    March 19, 2008

    I wonder if you can point me to the people doing the correcting dsm?

    Posted by: Michael X

    Recapitulation theory has been utterly discredited for quite a while:

    http://en.wikipedia.org/wiki/Recapitulation_theory

    This “yolk sac” genome crap is just an attempt to breathe life into it again.

  28. #28 Michael X
    March 19, 2008

    Yes, I’m quite familiar with Haeckel.

    As for “yolk sack genome crap”, I’m afraid you’ll have to do better than simply assert your conclusion that the claim is crap, on a blog post that identifies the evidence used to support the claim. As of yet you’ve left me unconvinced.

    In other words, take the hint from my original question and do what scientists do: science.

  29. #29 mayhempix
    March 19, 2008

    As usual, the “yolk” comes at the expense of IDrs and creationists.

  30. #30 kmarissa
    March 19, 2008

    Yeah, and we have gill slits, too, and resemble other animals while in the womb. Oh, no, wait. Those both have both been disproven. My bad.

    This is hilarious. You know, usually, we get the creationists on the posts that are actually about creationism or ID, not on the pure science ones. But there’s something even more amusing about a long and informative science-heavy post, complete with pictures, followed by the blogging equivalent of “LALALALA-I-CAN’T-HEAR-YOU-LALALA. You can’t teach me NUTHIN.”

  31. #31 Schmeer
    March 19, 2008

    Michael X,
    Don’t worry, dsmvwld comes by to troll lately. He won’t answer most questions, as we’ve seen in other threads. He was “indoctrinated” by “atheists” and managed to escape to the wonderful freedom of christianity. Excuse me I just threw up in my mouth a little.
    He refuses to detail what the doctrine forced on him might be. Don’t expect an answer to your question either.

  32. #32 Michael X
    March 19, 2008

    Thanks Shermer. That figures… I’ll still give the guy a chance to answer me though. And if he refuses to talk sense, I’ll simply defer to Troll Treatment Protocols.

    Although, I suppose I should have been tipped off by the handle “Disemvoweled?”… Yish.

  33. #33 Schmeer
    March 19, 2008

    Thanks Shermer.

    No Problem. However, I am significantly less famous than someone named Shermer.
    I was trying to figure out what the hell ‘dsmvwld’ was supposed to mean. I guess one of the inhabitants of the dungeon escaped.

  34. #34 Kevin Dorner
    March 19, 2008

    Oft-repeated but little-followed, Mr. Darwin’s advice again:
    “It appears to me (whether rightly or wrongly) that direct arguments against Christianity and theism produce hardly any effect on the public; and freedom of thought is best promoted by the gradual illumination of men’s minds which follows from the advance of science.”

    So, more posts like this please. :^)

  35. #35 Michael X
    March 19, 2008

    That’s hilarious! Sorry about that little slip, Schmeer. Besides, I’m sure you’re famous in your own right!

  36. #36 Joshua Zelinsky
    March 19, 2008

    Obviously, prior to the fall humans had yolks. It is very likely that they had both options, the ability to have live births or to lay eggs as necessary. After the fall, we know longer had the ability to lay eggs. This is of course consistent with Eve’s curse of childbirth! Your claimed evidence of evolution really supports the Bible!

    Ok, so I shouldn’t be giving the YECs ideas but it was too much fun to resist. I’ll go back to my little corner now…

  37. #37 Sickle Cell
    March 19, 2008

    Regarding soft tissue fossilization: how do soft tissue fossilize? I thought that the only reason we even got fossils is because the hard parts in dead animals can fossilize because part of their body is actually MADE of minerals.. How do you get minerals to preserve their shape?

  38. #38 Sili
    March 19, 2008

    Just here to Nth the cries of “Good job!”

  39. #39 Sickle Cell
    March 19, 2008

    “I love, love, love these kind of posts on Pharyngula. More please!!!”

    BTW – I think that PZ isn’t writing less posts about science than about creationism and hacks because he’s less interested in science,

    I just think it takes a lot more work to write about science than about dribbling idiots who just spew unimaginative lies all the time.

  40. #40 Abby Normal
    March 19, 2008

    dsm, did you read the entire wiki page you linked to, or only enough to validate your preconceived notions? I ask because the Modern Observations and Modern Theory sections significantly undercut your point and seem pretty simple to understand.

  41. #41 Mollie
    March 19, 2008

    dsmvwld, Haeckel’s theory of recapitulation isn’t the same as saying that embryos of many species look alike.

    Haeckel’s theory has been discredited in its strong form — human embryos don’t literally go through a “lizard” phase — but it’s absolutely beyond doubt that embryos of different species look alike. I’ve seen it myself with my own two eyes (and a nice dissecting microscope). Actually, I saw it yesterday.

  42. #42 Blake Stacey
    March 19, 2008

    Sickle Cell (#39):

    I just think it takes a lot more work to write about science than about dribbling idiots who just spew unimaginative lies all the time.

    I’ve found it so.

    Actually, to go into a little more detail (I’ve got a simulation running, so right now I have time to kill), the hardest posts to write are those in the middle. Pointing out the drool from a “dribbling idiot” is easy, and writing a technical post full of equations and other goodies for fellow specialists isn’t too hard, either. It’s popularizing something which hasn’t been popularized before that’s hard!

    Still, I try, because it’s also awfully fun.

  43. #43 carey
    March 19, 2008

    So you are telling me that the Big Designer went to the bother of designing copies of genes that look just like we would expect if there were an ungodly process called ‘evilution’?

  44. #44 Ichthyic
    March 19, 2008

    Now I’m curious, what pre-mammalian tissue evolved into the placenta?

    hmm, being an ichthyologist, my first thought would be to look to fish…

    http://icb.oxfordjournals.org/cgi/content/abstract/32/2/276
    http://www.sciencemag.org/cgi/content/abstract/298/5595/1018

    there’s quite a few published studies on placental fish, though I’m not entirely sure what the current consesus is as to exactly when this trait first appeared in fishes (despite the article I just linked to). Several studies suggest many independent, repeated evolutions of this trait in various lineages.

    some species of sharks also have a similar placenta-like structure, which also evolved well after the ostei/chondry split, just for comparison.

    Of course, I might just be stumping for fish (I’m biased that way), and there might be no relationship whatsoever as to what the basal tissues were that evolved into placentas in mammals.

  45. #45 Jared Lessl
    March 19, 2008

    #37 – how do soft tissue fossilize

    Fossilization of any sort is rare indeed. Maybe one organism in a trillion leaves any part of them behind for longer than a year. It requires a particularly special set of circumstances, and many species live in habitats that, barring bizzare accidents, are simply not conducive to making fossils. Chimpanzee ancestors, for instance, including our MRCE with them. We have basically none of those, since they were forest dwellers and their bodies didn’t end up in the sort of ground that could preserve them. Soft ground and sediments are very good, which is why he have so many marine fossils.

    Soft tissue fossilization works pretty much the same way, but it requires an even more extremely unlikely set of conditions. It’s like winning the lottery twice in a row with only two tickets. “Exquisitely rare”, is how Wikipedia describes it. Requires a nice anerobic environment and a steady supply of mineral-rich water.

  46. #46 Ichthyic
    March 19, 2008

    why isn’t dsmvld BEING disemvoweled at this point?

    the entire idiotic argument about Haeckel constantly rehashed by creobots was addressed thousands of times on various sites, so often it’s become part of the Index to Creationist Claims.

    Moreover, PZ also dealt with it in great depth not that long ago.

    I would suggest the-future-to-be-really-disemvoweled take his protestations of naught here:

    http://scienceblogs.com/pharyngula/2007/02/wells_and_haeckels_embryos.php

  47. #47 Dahan
    March 19, 2008

    Criminy! Even an artist/designer like myself can follow this. Nice explanation for us lay-folk PZ.

  48. #48 Torbjörn Larsson, OM
    March 19, 2008

    So you are saying that I, as a mammal, can be egg-static over reproduction?

    Figures. But nice to know, so I’m joining the choir here.

  49. #49 Torbjörn Larsson, OM
    March 19, 2008

    So you are saying that I, as a mammal, can be egg-static over reproduction?

    Figures. But nice to know, so I’m joining the choir here.

  50. #50 DarkSyde
    March 19, 2008

    Wow! That’s one of the most interesting posts I’ve ever read. In fact this may replace my all time pharyngula fave.

  51. #51 Jeffery Keown
    March 19, 2008

    I stand in awe of this process. We really are the past, writ tiny in the present. You just have to know where to look and then not turn away as so many do. Great Post!

  52. #52 Benjamin C
    March 19, 2008

    Hmmm Fossilized mammary glands.

    Would that be like a brick tit house?

  53. #53 alison
    March 19, 2008

    Wow, this is a wonderful post! I’ve passed the link on to my students in our evolution paper with a strong recommendation (heh heh test material…) that they read it.

    And I choked on my cuppa tea when I got to Benjamin’s crack about brick tit houses :-)

  54. #54 noncarborundum
    March 19, 2008

    … fossilized mammary glands …

    Why can’t I rid my mind of the image of Magda from There’s Something About Mary? Out! Out, I say!

  55. #55 AlanWCan
    March 19, 2008

    PZ, that was fantastic.
    When’s your book coming out?

  56. #56 CrypticLife
    March 19, 2008

    Now, if only babies came with bacon. It would be good for the mother (and father!) to have a little after-birth (or, if you prefer, afterbirth) sustenance.

  57. #57 Knight of L-sama
    March 19, 2008

    Nice, informative post that’s easy to follow, even for those of us who don’t do biology but I do have a slight complaint.

    We modern mammals don’t need yolk at all…

    Mammals don’t make vitellogenin at all…

    Shouldn’t these statements have qualifiers on them? Last I checked the monotremes were part of Mammalia, even if they are an outlying group.

  58. #58 Sven DiMilo
    March 19, 2008

    what pre-mammalian tissue evolved into the placenta?

    The eutherian placenta is derived mostly from the chorion and allantois, two of the other (besides yolk sac and amnion) extra-embryonic membanes in amniotes (the eggs of reptiles, birds, and mammals all have them). As I recall it’s different in marsupials, deriving from the chorion and yolk sac instead. Don’t see how these could be homologous to anything in sharks. Chorioallantoic placentas have evolved convergently, however, in lizards.

  59. #59 Ford
    March 19, 2008

    I understand why there’s a cross marking our Lutheran Ancestor, but what are the other crosses?

    Great post, actually.

  60. #60 David Marjanovi?, OM
    March 19, 2008

    The divergence dates of the tree are for the most part implausible. There’s a good fossil record of the Eutheria-Metatheria divergence… 125 million years ago, 130 perhaps, but never 180. 180 is where the Theria-Monotremata divergence should be put. Did you see how the tree implies that VIT2 was separately inactivated in the ancestry of primates and carnivores? The fossil record puts that divergence close to 65 million years ago, so VIT2 was probably inactivated just once, in the ancestry of Placentalia.

    Ironically, the 310-million-year date (actually 312) for the theropsid-sauropsid divergence is taken from the fossil record — but it’s the absolute minimum of a very badly constrained date! The maximum is somewhere around 335… People should really stop using this divergence as a calibration point.

    (And, as mentioned, monotremes are too mammals. And yes, stop codons signal the end of translation…)

    How do you get minerals to preserve their shape?

    Your question contains half of the answer. Fast decay can produce acids, which can precipitate minerals that happen to be around, et voilà.

    In really exceptional cases, namely the Tyrannosaurus blood vessels and not much else, decay is prevented altogether by… fast burial and dryness perhaps… that’s not well understood yet.

  61. #61 David Marjanovi?, OM
    March 19, 2008

    The divergence dates of the tree are for the most part implausible. There’s a good fossil record of the Eutheria-Metatheria divergence… 125 million years ago, 130 perhaps, but never 180. 180 is where the Theria-Monotremata divergence should be put. Did you see how the tree implies that VIT2 was separately inactivated in the ancestry of primates and carnivores? The fossil record puts that divergence close to 65 million years ago, so VIT2 was probably inactivated just once, in the ancestry of Placentalia.

    Ironically, the 310-million-year date (actually 312) for the theropsid-sauropsid divergence is taken from the fossil record — but it’s the absolute minimum of a very badly constrained date! The maximum is somewhere around 335… People should really stop using this divergence as a calibration point.

    (And, as mentioned, monotremes are too mammals. And yes, stop codons signal the end of translation…)

    How do you get minerals to preserve their shape?

    Your question contains half of the answer. Fast decay can produce acids, which can precipitate minerals that happen to be around, et voilà.

    In really exceptional cases, namely the Tyrannosaurus blood vessels and not much else, decay is prevented altogether by… fast burial and dryness perhaps… that’s not well understood yet.

  62. #62 David Marjanovi?, OM
    March 19, 2008

    I understand why there’s a cross marking our Lutheran Ancestor, but what are the other crosses?

    When a gene goes extinct, it receives a Christian funeral…

    Clicking on the picture gives you a large, readable version.

  63. #63 David Marjanovi?, OM
    March 19, 2008

    I understand why there’s a cross marking our Lutheran Ancestor, but what are the other crosses?

    When a gene goes extinct, it receives a Christian funeral…

    Clicking on the picture gives you a large, readable version.

  64. #64 HalfMooner
    March 19, 2008

    PZ, I salute you. This article, and particularly the following, were among the finest examples of popular science writing I’ve ever seen:

    “When non-functional genes, called pseudogenes, like this are found, one thing one can do is estimate the time of loss of function from the amount of decay. Natural selection is a force that maintains genes, and in its absence, they tend to slowly fall apart as they accumulate mutations. Browsing through the genome is like strolling through a run-down neighborhood. Houses that are still occupied will be maintained and kept up. Houses that have been recently abandoned might have an overgrown lawn and broken windows. Houses that have been neglected longer still might show signs of fire damage, or structural collapse, or might have been demolished right down to their foundations. By measuring the divergence of mammalian pseudogenes for vitellogenin from bird vitellogenin genes, for instance, we can estimate the time of loss.”

  65. #65 LisaJ
    March 19, 2008

    That was a great post! Thanks so much for that. I love these types of posts as well, you really do have a gift for explaining science in really exciting ways. Can I just pass along to you all the papers I need to read for my PhD research and have you summarize it so nicely for me? Thanks so much!

  66. #66 shane
    March 19, 2008

    So what came first? The pre-mammalian or the egg?

    Great post. Between the BA balancing eggs and PZ cracking a few eggs we have the best of scientificky stuff.

    Now can we get back to the religion bashing? ;-)

  67. #67 Keith Eaton
    March 19, 2008

    ” it’s a useless fluid filled space that contains no yolk at all, but is homologous to similar structures that form in birds and reptiles.”

    “Liar Liar pants on fire”

    A few adjustments via the Eaton BS filter:

    Definition of Yolk sac

    Yolk sac: Not all yolk has to do with birds’ eggs. Human embryos have a yolk sac, too. The human yolk sac is a membrane outside the embryo that is connected by a tube (the yolk stalk) though the umbilical opening to the embryo’s midgut. The yolk sac serves as an early site for the formation of blood and in time is incorporated into the primitive gut of the embryo.

    Gosh, Can it be that the http://www.medterms.com/script/main/art.asp?articlekey=6063
    medical community disagrees completely with PEE Zippo Myers…well yes actually it does.

    Even Wikipedia: aw you don’t say

    In humans
    The yolk-sac is situated on the ventral aspect of the embryo; it is lined by endoderm, outside of which is a layer of mesoderm.

    It is filled with fluid, the vitelline fluid, which possibly may be utilized for the nourishment of the embryo during the earlier stages of its existence.

    Blood is conveyed to the wall of the sac by the primitive aorta, and after circulating through a wide-meshed capillary plexus, is returned by the vitelline veins to the tubular heart of the embryo. This constitutes the vitelline circulation, and by means of it nutritive material is absorbed from the yolk-sac and conveyed to the embryo.

    Gee its not empty, oh it circulates blood in the developing baby, wow that doesn’t sound empty and useless does it.

    Take the so-called “yolk sac,” for instance. In chickens, the yolk contains much of the food that the chick depends on for growth. But we, on the other hand, grow attached to our mothers, and they nourish us. Does that mean the fetus’s so-called “yolk sac” can be cut off from the human embryo because it isn’t needed? Not at all. The “yolk sac” is the source of the human embryo’s first blood cells, and death would result without it.

    Gee death would result without it …hmmmmmmm (that empty useless sac)

    Now here’s an engineering problem for you. In the adult, you want to have the blood cells formed inside the bone marrow. That makes good sense, because the blood cells are very sensitive to radiation damage and bone would offer them some protection. But you need blood in order to form the bone marrow that later on is going to form blood. So, where do you get the blood first? Why not use a structure similar to the yolk sac in chickens? The DNA and protein for making it are “common stock” building materials. And, since it lies conveniently outside the embryo, it can easily be discarded after it has served its temporary-but vital-function.

    http://stemcells.nih.gov/info/scireport/appendixA.asp

    The primary roles of the human embryonic yolk sac are to initiate hematopoiesis and help in the formation of the primary germ cells, which will ultimately differentiate into eggs and sperm in the adult.

    http://www.medscape.com/viewarticle/465897_5

    The yolk sac is a primitive structure that usually disappears after 20 weeks’ gestation. A remnant of the yolk sac merges in the forming embryo into the primitive gut. The role of the yolk sac in early gestation is to supply the embryo with oxygen and nutrients until the formation of the placenta is accomplished. The yolk sac is also the first site of hematopoeisis, with embryonic red blood cells and macrophages visible in the yolk sac as early as 2 weeks’ gestation. Neutrophils, platelets, and lymphocytes are not produced in the yolk sac.[21] The allantois develops into a fibrous cord, the urachus, which runs from the fetal bladder to the umbilicus. This urachus can remain patent in the neonate with urine secreted from the umbilicus. The yolk sac and allantois are the only portions of the fetal membranes that develop to form a part of the fetus itself. The chorion and amnion are discarded after birth when their usefulness has ended

    See there’s a reason this dumb butt PZ is an isolated nobody in a pre-school on a frozen tundra away from any mainstream science. He’s full of crap.

    DO you sychophants ever check out this crap he posts?

  68. #68 raven
    March 19, 2008

    So what about all the other mammals. My reading of mammalian phylogeny implies that there were a lot of mammalian lineages, almost all of which died out.

    wikipedia evolution of mammals
    –Cynodonts

    |
    `–Mammaliformes

    |
    +–Allotheria

    | |
    | `–Multituberculates

    |
    `–+ -Morganucodontidae

    |
    `- -+–Docodonta

    |
    Hadrocodium

    |
    ` –Symmetrodonta

    |
    |–Kuehneotheriidae
    |
    `–Mammals

    Mammals seem to be just a twig on a large bush when you factor in the long life of our lineage. But even this twig has a wide diversity of reproductive strategies, egg layers, pouches, placentas. This might be an impossible question to answer but what about the multituberculates or the docodonta? Did they all just lay eggs or bear live young or what?

  69. #69 Sven DiMilo
    March 19, 2008

    Since all those branches occur before monotremes split off (they are true mammals), and monotremes and all other amniotes lay eggs (except for some derived lizards and snakes), the parsimonious inference (by phylogenetic bracketing) would be that they all laid eggs. But I don’t see how we’ll ever know whether live-bearing evolved in some of those lineages in parallel.

  70. #70 g
    March 19, 2008

    “It shows that nutritive lactation arose before placentation and loss of the vitellogenin genes.”

    This is important. Consider the alternative: what if the molecular clocks indicated that the yolk genes were lost before the lactation genes arrived? Was there an intervening period with neither nutrition method present? Probably not. Is the molecular clock experiment unreliable? Unfortunate if true. Was the whole thing not evolved after all? I don’t remember anything like this in Genesis.

    Instead, the data shows what would be expected of evolution: yolk nutrition did not disappear before a replacement was available.

  71. #71 raven
    March 19, 2008

    the parsimonious inference (by phylogenetic bracketing) would be that they all laid eggs. But I don’t see how we’ll ever know whether live-bearing evolved in some of those lineages in parallel.

    I would tend to agree with your logic. But recently I read a tome that pointed out that reproductive strategies seem to depend more on ecology than phylogeny.

    Sharks bear live young.
    Some snakes bear live young.
    Some mammals lay eggs.
    Sea horses brood eggs in pouches.

    One source said that multituberculates have pelvic anatomy that might indicate a marsupial type of reproduction with tiny young born after a brief gestation. But admitted that is wasn’t much to hang a theory on.

    I guess we may never know unless someone finds an internal fetal skeleton or egg clutch of one of these in a Burgess shale class lagerstatten.

  72. #72 Kseniya
    March 20, 2008

    Haeckel! Hitler! Cows becoming whales!

    Ok. I’m done.

  73. #73 Ichthyic
    March 20, 2008

    But recently I read a tome that pointed out that reproductive strategies seem to depend more on ecology than phylogeny.

    and can evolve quite rapidly, as well.

    which was one of the reasons i thought the links to the evolution of viviparity in fishes would be interesting.

    some lineages show multiple independent occurrences of viviparity, and it can evolve at least as rapidly as other traits like complex eyes.

  74. #74 Ichthyic
    March 20, 2008

    Haeckel! Hitler! Cows becoming whales!

    you forgot:

    PYGMIES AND DWARVES!!!!!

  75. #75 Sven DiMilo
    March 20, 2008

    some lineages show multiple independent occurrences of viviparity

    About 100 times in squamates alone!

  76. #76 Marc
    March 20, 2008

    Most informative thankyou

  77. #77 Lisa C.
    March 20, 2008

    I loved this post! So informative. Thank you.

  78. #78 Paul Flocken
    March 20, 2008

    Joshua Zelinsky–“Obviously, prior to the fall, humans had yolks. It is very likely that they had both options, the ability to have live births or to lay eggs as necessary. After the fall, we no longer had the ability to lay eggs. This is of course consistent with Eve’s curse of childbirth! Your claimed evidence of evolution really supports the Bible!

    Ok, so I shouldn’t be giving the YECs ideas but it was too much fun to resist. I’ll go back to my little corner now…”

    Considering how much the hebrew’s weather god hates sex, were those eggs fertilized internally, or externally?

  79. #79 Graculus
    March 20, 2008

    g: what if the molecular clocks indicated that the yolk genes were lost before the lactation genes arrived? … Instead, the data shows what would be expected of evolution: yolk nutrition did not disappear before a replacement was available.

    That’s not what is expected *at all*. Lactation occurs *after birth*. Yolk *and* placenta are *pre-birth* strategies. Lactation is a completely seperate issue having to do with the development stage of the animal *at birth*, not before. (Ever seen a breast inside of a womb?)

    Placental sharks rather obviously don’t lactate.

    Was there an intervening period with neither nutrition method present? Probably not.

    Being as at least one already exists, the probability is pretty high. Placental sharks have a method for nutrition that is neither yolk nor placenta. Before the placenta develops nutrition is secreted directly into the womb (although the yolk hasn’t completely disappeared at the early stages, it does provide a strategy whereby it could).

    Many sharks have cute little pre-birth trick… momma shark proves spare eggs for the young to eat while still in the womb… shark caviar.

    -(Not a biologist, just a shark fan.)

  80. #80 David Marjanovi?, OM
    March 20, 2008

    One source said that multituberculates have pelvic anatomy that might indicate a marsupial type of reproduction with tiny young born after a brief gestation.

    Yes (the pelvic canal is really small), but Wikipedia probably has the phylogeny wrong and the multis are probably more closely related to us than the monotremes are.

    That’s not what is expected *at all*. Lactation occurs *after birth*. Yolk *and* placenta are *pre-birth* strategies. Lactation is a completely seperate issue having to do with the development stage of the animal *at birth*, not before.

    No: marsupials are born at a much earlier stage than monotremes hatch (and even these hatch quite early, like highly altricial birds AFAIK). That placentals spend the fetal stage in the womb instead of in a pouch is probably a secondary development.

    Keith Eaton, did you notice how self-defeating your point is? Fine, so the yolk sac is not useless — it still produces blood cells like it does in all other vertebrates! Yet another thing we have in common. Why should that be? Perhaps we all share a common ancestor? Hey, why don’t we produce our first blood cells in the placenta?

    Keep asking “why”. Science is about “why” questions. All those people who say science is only about “how” and philosophy and/or religion are about “why” don’t know what they’re talking about.

  81. #81 David Marjanovi?, OM
    March 20, 2008

    One source said that multituberculates have pelvic anatomy that might indicate a marsupial type of reproduction with tiny young born after a brief gestation.

    Yes (the pelvic canal is really small), but Wikipedia probably has the phylogeny wrong and the multis are probably more closely related to us than the monotremes are.

    That’s not what is expected *at all*. Lactation occurs *after birth*. Yolk *and* placenta are *pre-birth* strategies. Lactation is a completely seperate issue having to do with the development stage of the animal *at birth*, not before.

    No: marsupials are born at a much earlier stage than monotremes hatch (and even these hatch quite early, like highly altricial birds AFAIK). That placentals spend the fetal stage in the womb instead of in a pouch is probably a secondary development.

    Keith Eaton, did you notice how self-defeating your point is? Fine, so the yolk sac is not useless — it still produces blood cells like it does in all other vertebrates! Yet another thing we have in common. Why should that be? Perhaps we all share a common ancestor? Hey, why don’t we produce our first blood cells in the placenta?

    Keep asking “why”. Science is about “why” questions. All those people who say science is only about “how” and philosophy and/or religion are about “why” don’t know what they’re talking about.

  82. #82 David Marjanovi?, OM
    March 20, 2008

    No: marsupials are born at a much earlier stage than monotremes hatch (and even these hatch quite early, like highly altricial birds AFAIK). That placentals spend the fetal stage in the womb instead of in a pouch is probably a secondary development.

    I should have explained what my point is: Normal amniotes spend the fetal stage in the egg and live off yolk. Marsupials, and probably live-bearing mammals generally, spend the fetal stage in the pouch and live off milk. Thus, milk is a yolk replacement, with monotremes representing the intermediate condition. That placentals spend the fetal stage in the womb and live off blood is a later development — a third strategy.

  83. #83 David Marjanovi?, OM
    March 20, 2008

    No: marsupials are born at a much earlier stage than monotremes hatch (and even these hatch quite early, like highly altricial birds AFAIK). That placentals spend the fetal stage in the womb instead of in a pouch is probably a secondary development.

    I should have explained what my point is: Normal amniotes spend the fetal stage in the egg and live off yolk. Marsupials, and probably live-bearing mammals generally, spend the fetal stage in the pouch and live off milk. Thus, milk is a yolk replacement, with monotremes representing the intermediate condition. That placentals spend the fetal stage in the womb and live off blood is a later development — a third strategy.

  84. #84 howard hershey
    March 20, 2008

    Now I’m curious, what pre-mammalian tissue evolved into the placenta?

    There is an interesting ‘progression’ of the relationship between the embryonic chorion (the chorioallantoic sac forms the basis of the embryonic side of the placenta) and the maternal uterine tissues.
    In the most ‘primitive’ state, there are 6 layers between the maternal blood supply and the embryo’s blood supply: Going from mom to parasite — 1) uterine vascular endothelium, 2) uterine stroma, 3) uterine epithelium, 4) fetal trophoblast, 5) fetal stroma, 6) fetal capillary endothelium.
    Mammals that retain all 6 layers include some, but not all ungulates (pig, horse), whales, and lemurs. This is called an epitheiochorial placenta.
    In other species, the uterine epithelium is destroyed by the invading fetal trophoblast. Cows and sheep have this type of placenta, called syndesmochorial.
    Then we have placentas where the invading trophoblast removes the maternal connective tissue. Such plancentas are called endothelial-chorial. Carnivores, sloths, shrews and moles, and some bats have this type of placenta.
    The next-to-last type of placenta has the parasite’s trophoblast tissue in direct contact with the maternal blood tissue. This is the most intimate contact one sees between maternal and fetal blood supplies and is called a hemochorial placenta. Rodents, monkeys and great apes, including humans, have this type of placenta.
    In lagomorphs (rabbits), some rodents (rat), and the guinea pig, close to the end of gestation, the trophoblast syncitia also disapears or becomes highly reduced in width. This produces what is sometimes called a hemoendothelial placenta.
    In fact, all of the above can show various amounts of intermediacy. And with the change in type of placenta, there is also a change in the type of nutrients, from secretions to blood-borne.
    In short, there is substantial lineage-specific variation in the degree of intimacy between maternal and fetal tissues and that even includes whether chorion or yolk sac is involved.
    In addition to the placenta, in some insectivores and carnivores, there are pockets of extravascular maternal blood pooling in hematomas along the border of the placenta which is absorbed by the chorionic epithelium. This seems to be an important source of iron.
    Rodents, in addition to the chorionic placenta, *also* have a well-developed yolk sac placenta which absorbs secretions from the mother.
    Much of the above came from an old (40 years) source, but I would guess that most of it remains true.

  85. #85 trrll
    March 20, 2008

    Gee its not empty, oh it circulates blood in the developing baby, wow that doesn’t sound empty and useless does it

    Uh, the blood circulates through the wall of the sack, not the inside of it. And how about the damaged yolk protein genes? What use do you imagine for those?

  86. #86 prof weird
    March 20, 2008

    Keith Eaton staggers onto the board and vomits up :

    ” it’s a useless fluid filled space that contains no yolk at all, but is homologous to similar structures that form in birds and reptiles.”

    “Liar Liar pants on fire”

    A few adjustments via the Eaton BS filter:

    Translation : cherry picking extraneous data so Keith has a reason to posture and insult people.

    You really SHOULD try reading for comprehension and understanding of CONTEXT, rather than points to impotently rage about.

    The human yolk sac is useless – AS A SOURCE OF NUTRIENTS. Which is kinda the WHOLE POINT of the article.

    But I suppose you ‘overlooked’ those inconvenient facts in your desire to posture and pose like someone whose opinions actually matter ….

    Even your OWN cites show you are full of hot air :

    Take the so-called “yolk sac,” for instance. In chickens, the yolk contains much of the food that the chick depends on for growth. But we, on the other hand, grow attached to our mothers, and they nourish us. Does that mean the fetus’s so-called “yolk sac” can be cut off from the human embryo because it isn’t needed? Not at all. The “yolk sac” is the source of the human embryo’s first blood cells, and death would result without it.

    Gee death would result without it …hmmmmmmm (that empty useless sac)

    Let’s see : chicken’s yolk sac is mostly nutritive, plus a few other functions. In humans, yolk sac is virtually useless for nutrition, but still has the other functions.

    Now here’s an engineering problem for you. In the adult, you want to have the blood cells formed inside the bone marrow. That makes good sense, because the blood cells are very sensitive to radiation damage and bone would offer them some protection. But you need blood in order to form the bone marrow that later on is going to form blood. So, where do you get the blood first? Why not use a structure similar to the yolk sac in chickens? The DNA and protein for making it are “common stock” building materials. And, since it lies conveniently outside the embryo, it can easily be discarded after it has served its temporary-but vital-function.

    In other words, the function of the yolk sac CHANGED DURING EVOLUTION – before, it was mostly nutrient supply plus a few other functions; now, in humans it is mostly just those few other functions.

    You can justify whining about PZ over this HOW ?

    Your ‘explanation’ of why humans have badly damaged yolk protein genes when human embryos DON’T HAVE YOLKS is what again ?

    Your OWN references accord with evolution – the human yolk sac is PRIMITIVE feature that gets resorbed (like the tail/coccyx).

    Initiating Zeppelin Ego routine :

    See there’s a reason this dumb butt PZ is an isolated nobody in a pre-school on a frozen tundra away from any mainstream science. He’s full of crap.

    And WHO are you again ?

    Too bad he’s probably done more REAL science in his spare time than you have done in your entire life.

    If he’s so isolated, WHY are you so vitriolic ?

    What he does for a living IS mainstream science, twit. Upon what basis (other than to be a screeching cockalorum) would you claim otherwise ?

    DO you sychophants ever check out this crap he posts?

    Yes; it’s how we determine that he is right and you are, at best, a fabiform philodox.

  87. #87 trrll
    March 20, 2008

    Recapitulation theory has been utterly discredited for quite a while

    The notion that development is required to recapitulate adult features of a species’s evolutionary predecessors was abandoned long ago. It never really had a logical basis in terms of evolutionary theory, anyway.

    What remains is the recognition that features of embryonic development from evolutionary predecessors may be retained. This is expected because natural selection doesn’t get to redesign development from scratch as an “intelligent designer” might reasonably be expected to do–it has to work by modification of what is there before. Nor will natural selection necessarily choose the most efficient place to modify a developmental sequence; it is more likely to choose the changes that can be made most simply without loss of fitness, even if leaves redundant vestiges of the earlier developmental sequence, such as structures (e.g. “gill slits” or tails) that appear and then are reabsorbed without accomplishing anything useful.

    In particular, if a developmental feature like a yolk sac has evolved any other useful functions other than storing yolk–even minor ones–the morphology of the sac is likely to be retained in development after the yolk producing function has been lost, even if those functions do not logically require a sac-like structure.

  88. #88 Ichthyic
    March 21, 2008

    Many sharks have cute little pre-birth trick… momma shark proves spare eggs for the young to eat while still in the womb… shark caviar.

    and some even produce enough young that they can cannibalize each other in the womb after they have hatched from the eggs.

    Now THAT’S some serious sibling rivalry.

    http://www.elasmo-research.org/education/topics/lh_intrauterine_cannibalism.htm

    not a bad shark site, btw, if you haven’t seen it yet.

  89. #89 Reepicheep
    March 22, 2008

    Aha! Now I know what to celebrate as we color our Easter eggs tonight with the kids. As a non-Christian, I have found other reasons to celebrate on this day, and now I can add this to my list. Tomorrow I celebrate spring, birds, birth, bunnies and reproduction, and the egg yolk genes present in human DNA. (Maybe that’s the origin of “Mother Goose?” Hmmm . . . something to that Jungian Collective unconcious after all?)

  90. #90 Mary
    August 15, 2008

    excellent! I work with Vitellogenin of tropical fish and I really enjoyed this article and the revision that make.. thanks!!

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