Thursday, December 22, 2011

The Cambrian Conundrum: Fossils vs Genes

The earliest fossil examples of most animal classes and phyla appear in the fossil record at about the same time in the Cambrian (about 530 million year as ago (Ma)). This period of apparent rapid divergence is referred to as the "Cambrian Explosion."

It seemed unlikely that this disparity could have evolved in just a few million years so many scientists have been searching for fossil antecedents in the early Cambrian and Ediacaran (635-541 Ma). Many trace fossils have been found in the past few decades, indicating that the fossil animals of the Cambrian were preceded by small wormlike creatures.

The other approach has been sequence analysis. One can construct molecular phylogenies by comparing the sequences of genes in modern extant organisms. This approach has been highly successful over the past fifty years so that we now know a great deal about the relationship of the various animal phyla. The correspondence between the old morphological taxonomy and molecular evolution is the most powerful evidence we have that evolution explains the history of life [see Twin Nested Hierarchies].

The problem with sequence comparisons has always been getting accurate dates using the molecular clock. It is hard to get an accurate date when dealing with events that occurred 500 million years ago because there aren't very many calibration points. An accurate calibration point is a known time when two lineages diverge.

If there really was a rapid divergence in the Cambrian then one would expect the molecular tree to show this. But it never has. The molecular phylogeny shows that chordates diverged from invertebrates at least one hundred million years before their fossils appear in the Cambrian. Similarly other phyla and classes of animals have their origin long before the Cambrian, according to the molecular clock.

A recent paper in Science extends this comparison by calculating more a more accurate molecular phylogeny using seven housekeeping genes from 118 different species (Erwin et al. 2011). The result is shown in Figure 1 of the paper: "The origin and diversification of animals as inferred from the geologic and genetic fossil records." (Click on the figure to embiggen.)


This is a complicated figure. The fist part shows the rise of new phyla (blue) and new classes (yellow) over time. The scale of taxa numbers is on the left. The rapid rise in the number of phyla and classes, as measured by the fossil record, is evident at the beginning of the Cambrian era (green bars on the y-axis).

The molecular tree is shown as an overlay with the various species on the right-hand x-axis. As you can see, the branch points (nodes) for the various classes and phyla pre-date the Cambrian by millions of years. There is no obvious correlation between the fossil record and the phylogeny.1

The authors refer to this difference as the "Cambrian Conundrum." The problem has been apparent for about 25 years and it seems no closer to being solved than it was in the 1980s. The only difference is that now developmental biology has show us how easy it is to evolve very different organisms with only small changes in regulating gene expression. That part isn't a problem. Whether these developmental changes were triggered by environmental changes, such as the oxygenation of the oceans or the rise of predators, remains an open question.

Here's the abstract of the paper.
Diverse bilaterian clades emerged apparently within a few million years during the early Cambrian, and various environmental, developmental, and ecological causes have been proposed to explain this abrupt appearance. A compilation of the patterns of fossil and molecular diversification, comparative developmental data, and information on ecological feeding strategies indicate that the major animal clades diverged many tens of millions of years before their first appearance in the fossil record, demonstrating a macroevolutionary lag between the establishment of their developmental toolkits during the Cryogenian [(850 to 635 million years ago (Ma)], and the later ecological success of metazoans during the Ediacaran (635 to 541 Ma) and Cambrian (541 to 488 Ma) periods. We argue that this diversification involved new forms of developmental regulation, as well as innovations in networks of ecological interaction within the context of permissive environmental circumstances.


1. Note that this does not conflict with the twin nested hierarchies. It's a different problem—one that deals with dates and not relationships.

Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D., and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [PubMed] [doi: 10.1126/science.1206375]

12 comments :

  1. My take on punctuated equilibria is that there can be steady gradual genotype change, but rapid bursts of phenotype change.

    The fossil record mainly shows phenotype evolution, while the molecular clock data is related to genotype evolution. Over sufficiently long periods, the two should line up, but that still allows some bursty behavior in phenotype evolution.

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  2. > nwrickert: Over sufficiently long periods, the two should line up, but that still allows some bursty behavior in phenotype evolution.

    But not explosive behavior? The conundrum is not burstiness, it seems, but the quantity of the burst.

    Surely there was not a huge amount of ready-to-diverge to such extraordinary speciation in the genome, hidden away until say, the ice melted.

    And to think, the naturalists accuse ID of Deus ex machina!

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  3. "But not explosive behavior?"

    I don't see why not.

    There's already a population (or populations) with a lot of variation. With the crossovers that occur during meiosis a population is, in effect, a recombinant DNA laboratory. The "explosion" would come from the combinatorial explosion, with the huge number of possibilities it can produce. New mutations would not be required.

    Normally, you would not see this happen. But at a time of rapid environmental change, there are lots of potential new ecological niches opening. All it takes is for a particular combination to find itself in a new niche where it can flourish.

    Later natural selection would refine the new lines to their new niches, and later mutation would replenish the variation of the populations. But an explosion itself should be possible from existing variation whenever there are rapid environmental changes.

    If the human population manages to destroy itself with the global warming, it might be setting up the conditions for another future "explosion."

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  4. lee merrill writes:

    And to think, the naturalists accuse ID of Deus ex machina!

    As Dr. Moran says, "naturalists" don't consider the issues regarding the timing of genealogy vs. morphology in the Cambrian and preceding eras to have been answered by a long shot, so there's a great deal of interesting research going on regarding these issues.

    When ID sees things like the Cambrian "explosion," it says "God musta done it since we can't think of a good enough alternative explanation." "Naturalists" say "We can't think of a good enough explanation, sounds like a really interesting question! Let's see what more we can find out!"

    See a difference there?

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  5. Looking at the cladogram you almost can't detect any Cambrian explosion. If anything it looks like there's an explosion in the 'Cryogenian' (that's a new one to me). Is it possible that the cambrian expl. just represents a preservation bias? If the cryogenian is really cold, that should increase the ocean's ability to hold CO2, maybe it held it so tightly that these organisms couldn't biologically precipitate calcite to make hard parts, but afterwards there's a plethora of preservable material?

    Also, doesn't this really just mean that these lineages become isolatated from one another at that time, not necesarily that these different body plans actually existed? If we traveled back in time to the Cryogenian, would we be seeing Ur-cephalochordates competing with Ur-brachiopods? Or would we just see a bunch of squishy things that are fairly similar because they're only fairly recently diverged? The genetics is telling us when they seperated, but not when the body forms developed no?

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  6. Schenck said: Looking at the cladogram you almost can't detect any Cambrian explosion. If anything it looks like there's an explosion in the 'Cryogenian' (that's a new one to me). Is it possible that the cambrian expl. just represents a preservation bias? If the cryogenian is really cold, that should increase the ocean's ability to hold CO2, maybe it held it so tightly that these organisms couldn't biologically precipitate calcite to make hard parts, but afterwards there's a plethora of preservable material?

    Sounds reasonable to me. Interestingly, there seem to be two minor bursts of gene-birth, one following the Cryogenian and another going into the Cambrian according to this excellent article on a Nature paper: (Go to the graph) http://pandasthumb.org/archives/2011/04/the-true-story.html

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  7. The biggest problem is that genes alone do not explain why we see such an explosion of morphological diversity during the Cambrian. This is because complex anatomies are not themselves encoded in DNA.

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  8. @lee merrill

    And to think, the naturalists accuse ID of Deus ex machina!

    No, just willful or contrived ignorance and dishonesty.

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  9. My take on punctuated equilibria is that there can be steady gradual genotype change, but rapid bursts of phenotype change.

    No, that's mostly evo-devo mumbo jumbo. The problem is that you can have near identical genomes in organism that are morphologically different to a great extent.

    Genes and DNA do not themselves determine anatomies.

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  10. Atheistoclast said...
    The problem is that you can have near identical genomes in organism that are morphologically different to a great extent.

    Please define "near-identical" and "morphologically different". Otherwise you are just talking bull$hit.

    The differences between us great apes is less than that between us and insects. "Genome identity" follows a similar pattern. And almost every study done on genetics of development supports this as a causative correlation.


    This from the guy trying to call Larry as using an "argument from ignorance" regarding transposable elements? Get real.

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  11. "The problem is that you can have near identical genomes in organism that are morphologically different to a great extent."

    A one percent difference in a 3 billion base pair genome is still 30 million bases. This not a big enough number for you?
    YECs no doubt think all these are functional too

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  12. I see that it has already been mentioned, but if one wants yet another perspective on diversity over time one can look at gene families. The real business is going on back in the Archean Expansion.

    And re merrill and Atheistoclast comments, there is still creationism out there? Amazing, since their ideas has been falling to natural selection on the market place of ideas. That confirms that the religious woo woo woo is that keeps the faithful at it.

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