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New genomes hint at evolution’s slimy past

RICE/ UC BERKELEY (US) — Scientists have unveiled the genomes of a leech, an ocean-dwelling worm, and a limpet, more than doubling the number of genomes from a vast, under-studied swath of the animal kingdom.

Lophotrochozoans, (pronounced “LOH-foh-troh-coh-zoh-uhns”), are a diverse group of animals that includes mollusks—such as snails, clams, and octopuses—and annelids—such as leeches and earthworms. This group includes as many as one-quarter of Earth’s marine species.


This scanning electron microscope image shows an 18-hour-old trochophore of the owl limpet, Lottia gigantea. (Credit: Eric Edsinger-Gonzales, UC Berkeley)

“Through comparison of these diverse genomes with each other, we can learn what animals have in common with each other, which in turn tells us about the features that their common ancestors had,” says Daniel Rokhsar, University of California, Berkeley, professor of molecular and cell biology and of physics.

“That is a big driver for comparative genome sequencing—it is one of the few ways we have of looking back in deep time.”

For these organisms, deep time means more than 500 million years ago, toward the end of the Precambrian era, when they split off from animals that eventually evolved to become vertebrates (animals with backbones), such as humans.

Most animals, including people, have body plans with bilateral symmetry, which means they have left and right sides that are mirror images of one other,” says co-author Nicholas Putnam, assistant professor of ecology and evolutionary biology at Rice University. “When you look at all bilaterian species, you can divide them into three big groups that biologists call clades.

“Lophotrochozoans are one of these clades, and when we looked at all of the genomes that had been sequenced, we found that only two were lophotrochozoans,” he says. “That left a big hole in the genetic record, and our goal with this study was to fill in some of the gaps in that blank space.”

Genome sequencing for the new study was performed at the Department of Energy’s Joint Genome Institute in Walnut Creek, California, where Rokhsar is program lead for eukaryotic genomics. As reported in Nature, the three newly sequenced species are Capitella teleta, an ocean-dwelling worm; Helobdella robusta, a freshwater leech; and Lottia gigantean, a large marine mollusk.


One of the latest three sequenced genomes belongs to the ocean-dwelling worm Capitella teleta, seen here. View larger. (Credit: E. Seaver/University of Hawaii)

Finding ancestors

“At Rice, we work on comparative genomics,” Putnam says. “We look for recognizable similarities across genomes, and we are interested in similarities among the genes themselves and also among the patterns of genetic organization. These structural similarities can tell us a lot about the evolution of individual genes and functional gene groups, like chromosomes.”

In examining the lophotrochozoan genomes, Putnam’s group developed new computational tools to examine and compare the differences among the three new genomes and hundreds of known genomes, including those for humans and oft-studied model organisms like the fruit fly.

The tools streamlined the search for similarities among the genomes and also helped the researchers trace evolutionary changes that occurred in specific groups of genes.

“Using these tools, we focus on the part of the evolutionary tree where specific mutations took place,” Putnam says. “For example, we can say, ‘A mutation occurred here that moved a big chunk of this chromosome, and it must have happened after lophotrochozoans diverged from deuterostomes but before the split between mollusks and annelids.’”

So far, Putnam’s group has traced 17 “ancestral linkage groups,” large groups of genes that are similar in structure to chromosomes, to the last common ancestor of all the bilaterians.

Genes today

“For us, the interesting thing is finding genes that exist today in different species, tracing those to a single gene in a common ancestor and then using the patterns we find to test hypotheses about evolutionary processes,” Putnam says. “Sometimes the genes today might still have the same function, but other times they have evolved an entirely new function.”

Putnam says the team has been able to trace the lineage of almost half of the genes in the three new genomes, and the work continues.

“These studies teach us important lessons about ourselves and other vertebrates,” Putnam says. “Looking across the animal kingdom gives us more resolution and clarity about what in our genome is new and what has been preserved from our ancient ancestors.”

Additional co-authors contributed from Rice, UC Berkeley, the European Molecular Biology Laboratory, JGI, Williams College, Children’s Hospital Oakland Research Institute, Hudson Alpha Institute for Biotechnology, and the University of Hawaii.

The DOE, the Gordon and Betty Moore Foundation, R. Melmon, the National Science Foundation, the National Institutes of Health, the Boehringer Ingelheim Fonds, and the National Human Genome Research Institute supported the research.

Sources: Rice, UC Berkeley

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16 Comments

  1. Roy Niles

    Some day these researchers will come to realize that these mutations were caused at least in part by the strategic functions of the organisms. Mutations by pure accident don’t confer intelligent changes that would otherwise need a miracle to intelligently fit new environmental circumstances. The organism’s intelligent functions are needed to take advantage of either accidental or self engineered mutations. Fast, slow or incredibly dumb, all organisms would not survive or evolve without some form of intelligence.

  2. Mark

    @ Roy Niles

    Mutations that fit new environmental circumstances are advantageous, therefore they aid the survival of this organism in these circumstances, helping to ensure that they are passed on through successive generations . There doesn’t need to be any ‘intelligent’ thinking or strategy behind it.

  3. Roy Niles

    Mark believes that accidents have advantageously intelligent results, and the organism never knew what hit it.

  4. Pete

    @ Roy Niles

    “Some day these researchers will come to realize that these mutations were caused at least in part by the strategic functions of the organisms.”

    Cool. I must say, your idea (a novel mechanism for guided alteration of DNA sequence) is a new one on me. How did you find out about this? In your armchair?

  5. Roy Niles

    No, I was standing up at the time.

  6. Frank

    @Roy as humans we have DNA machinery that will check to make sure all the nucleotides are paired up correct and that no errors are made, yet it isn’t 100% accurate and so there are mutations that occur, given the number of cells we have and how often cells divide (numbers not as high for other animals but still significantly larger than single-celled organisms) mutations will happen, sometimes they are fatal (and the mutated info is not passed on) and sometimes it makes a protein just a bit better at what it does and is therefore more likely to help the organism and for the mutation to be passed on.

    In your theory where an organism makes a strategic decision to mutate itself, in order for this mutation to be passed on (rather than die off) it would need to either a) be present in the reproductive organs (sperm, egg etc) or b) need to be developed early on in life and would then be present in all the cells (which would include the reproductive pathways).

    In the case of b, I would argue that such a mutation is occurring so early in the life that (at least for larger multicellular organism so as animals we see today) the organism hasn’t lived and experience life sufficiently and doesn’t have active control over the mutation and so it could not have been an intelligent function by the organism.

    In the case of a, for humans females have all their eggs very early on in their life and so the genetic material present in those eggs will be similar (if not exact) to the genetic material of an early age (and so would follow the logic from b above). Males however make sperm throughout their life, yet sperm is developed form germ cells set aside early in development. Without some kind of scientific proof that the organism is consciously or intentionally going back and modifying the eggs/germ cells, I don’t think anyone would be inclined to believe your theory.

    I am curious if you have refuted a similar argument in your published book.

  7. Roy Niles

    Frank, my arguments are supported by a number of prominent scientists who are often referred to as adaptive mutation theorists, and so I didn’t come up with these ideas on m own, I do quote these people in my book, but the book is mainly about my own ideas concerning the functional aspects of trust and its counter function of deception. And when all of these scientists speak of intelligent aspects of mutation, we don’t mean conscious acts of our more rational brains but the unconscious machinations of the intelligent processes that operate in every biological cell of every system.
    I repeat that mutations by pure accident don’t confer intelligent changes that would otherwise need a miracle to intelligently fit new environmental circumstances. NeoDarwinist theories such as yours recited here just can’t pass that simple test.
    Your little lecture about how sperm cells work and can’t be changed, etc., is simply wrong, and the newer study of epigenetic systems, for example, should have shown you that already. But I don’t intend to argue further about why your theories, no matter how cleverly designed over the years by scientists, simply cannot work. Oddly enough, the silly Creationists have pointed out a lot of your errors for many years, but they failed to come up with any better answers as well, giving credit for intelligence to gods instead of life. But life has been intelligent from the start, and no gods were needed. Where did we get that initial intelligence? That’s also a subject in the book.

  8. Roy Niles

    Frank, Read this piece and tell me how accidents created this arrangement:
    http://money.cnn.com/gallery/technology/2013/01/15/hardest-computing-problems.fortune/3.html

  9. Roy Niles

    Also, Frank, everything that uses a minimum of intelligence to do something is conscious on that level of what it has to feel to do it.
    That’s not in the book but it should have been.

  10. Roy Niles

    And check this out for the use of “intelligence” with reference to molecules:

    http://www.nano-initiative-munich.de/news/news/article/1/a-single-molecule-in-sight/

  11. Frank

    @Roy I’m having some trouble trying to grasp what exactly you mean by “intelligent processes that operate in every biological cell of every system” or by the “test” that NeoDarwinism theories can’t pass

    I am interested in the research showing that my understanding of epigenetics is flawed, despite that fact that post-translation modifications can have an effect on protein expression, the underlying DNA, which by the way would code for the very proteins that would perform the modifications, stays the same and is unaltered. So even if external factors cause modifications, the modifications would need to include changing DNA otherwise the offspring will have the exam same DNA and in the same environment respond in the same manner. If you think that enough code is built into DNA for a species to be able to adapt solely by post-translational modification to any environment, I would just point to any mass extinction where a majority of life was unable to cope with the quick change in environment. But with proof I would be inclined to believe you so just let me know where the proof is.

    If a given process happens an uncountable number of times (cell division for example), even with a mutation rate of 0.0001% statistically there will still be lots of mutations. Some will not have any effect (as many codons code for the same amino acid), some will have detrimental effects (most likely leading to death of the cell), and some will have beneficial effects (which would help the survival of the organism and increase the chance it reproduces). The fact is that random mutations would create a spectrum of variants for any specific thing you look at, and that environmental pressure will then select those variants that are favorable and select against those that are disfavorable. Considering how prevalent the Darwinian theory of evolution is and how widely accepted as the main theory of evolution due to a multitude of scientific vetting, I would actually say that in order to prove your alternate theory you would have to disprove other contradictory theories.

    I fail to see how Creationists are relevant to the conversation nor how they have disproved scientific literature, but as before solid proof is welcomed. The reason scientific theories are called theories is that there is evidence to support said theory. We might not be able to completely explain what a graviton is at this point in time, but the theory of gravity and attraction of two objects has been proven time and again.

    Check your links, I don’t see how either of those are relevant to this discussion. To me they both seem like using intentional design of a framework to achieve a specific goal.

    The only thing mentioned by adaptive mutation theorists that might help your case is that certain environmental pressures will increase the mutation rate, which will create more adaptions. I fail to see how such mutations would be locally limited to a specific region, but would swallow my words with sufficient proof. A phrase I am fond of is “Extraordinary theory, extraordinary proof” and so I await your extraordinary proof.

    Lastly, I just want to ask if I mixed a glass of water and a glass of oil together, watched as they exerted a force on the other (something I would deem external) and separated into two layers, would they be considered intelligent because the two liquids responded to outside stimuli?

  12. Roy Niles

    Frank, I presume you’re capable of doing your own (and actual) research into adaptive mutation. I’d also advise you to read my book except that if you wanted to you already would have. In any case there are a number of papers that speculate as to how the information in the DNA and RNA structures can be altered when experience is interpreted strategically and “advises” the systems to react with some retuning. And further papers examine the methods that the new strategic information can be transferred via sperm, etc.
    (Strategies that really can’t be accidentally mutated of course.)
    You state that “The only thing mentioned by adaptive mutation theorists that might help your case is that certain environmental pressures will increase the mutation rate, which will create more adaptions”
    That statement is clearly false, and you either haven’t read that anywhere in the works of any of those actual theorists or didn’t understand at all what you were reading.. So I suspect you just want to successfully argue, no matter if it’s a truthful argument or not.
    And why did I mention creationists? Because if you actually read any of their stuff, you’d see that they’ve done the math at least that tends to blow your statistic projections out of the water. Other than that they seem to making up as much stuff as you are now attempting to do.
    And then you come up with the silly oil and water analogy, which obviously has nothing to do with intelligent choice making creatures. These liquids are reacting rather than responding and bear no analogical relation to the molecular substances’ strategies in the cited article. Although if they did, you’d be even more wrong about the prevalence of intelligence in nature than you already are.

  13. rac

    We know that what we call intelligence exists in the higher orders of organisms. What is to say that it is not also present in lmore elementary ones? In any event, a question basic to the discussion is that of where / how intelligence was first acquired by the first “intelligent” organism? What we call intelligence, even at its most elementary level, is dependent upon the ability to acquire and process complex information. That this ability arose spontaneously by pure random chance either out of the primordial ooze or in the course of evolution is a flight of highly fanciful conjecture without substance.

  14. Frank

    “I presume you’re capable of doing your own (and actual) research into adaptive mutation. I’d also advise you to read my book except that if you wanted to you already would have.”

    Both true, yet neither provide evidence for your points nor discredit mine.

    My understanding of adaptive mutation comes from wikipedia (http://en.wikipedia.org/wiki/Adaptive_mutation), where discussion of increased mutation rates across the board take up a majority of the article.

    The “intelligent” polymer that you linked is simply performing a little thermodynamic process called osmosis (http://en.wikipedia.org/wiki/Osmosis). By using oil and water I was asking whether their separation, another process driven by entropy (a base tenant for thermodynamics), would also qualify as being “intelligent.” The fact you can’t comprehend the analogy leads me to question your logic skills. Additionally the two liquids do not react, a process implying that at least one of the compounds transforms into another. They are simply interacting with their surroundings and changing their shape into a conformation that is more favorable.

    If you are going to go around positing new/different theories that are at odds with the currently accepted and scientifically vetted theory then you ought to be able to back your theory up, plain and simple.

  15. Roy Niles

    So Frank, you look in Wikipedia to understand adaptive mutation? How logically skilled is that? And in your so-called understanding of your own analogy, your logic tells you that interaction does not involve reaction?
    All reactions in nature are governed by its intelligently evolved processes. John A Wheeler, physicist ,will have told you that as well as A. N. Whitehead, philosopher. Several others could be mentioned as well, but since you get your scholarly data from Wikipedia, there’d be no point.
    Take a look at this study by the way where we see some evidence that microbes are intelligent creatures – another thing that I recall you doubted: http://www.sciencedaily.com/releases/2013/01/130118172335.htm
    In short, I would argue that the reacting processes of the so-called non loving substances are nevertheless intelligently reactive and that those of the clearly living entities are intelligently proactive.
    But then of course at the level of your logic, you wouldn’t.

  16. Roy Niles

    By the way Frank, you sly fellow, the Wikipedia article includes this notice:
    “This article has multiple issues. Please help improve it or discuss these issues on the talk page.
    This article needs additional citations for verification. (May 2008)
    This article is written like a personal reflection or essay rather than an encyclopedic description of the subject. (May 2008)”
    As to articles re adaptive mutation, look up the writings of James A Shapiro, and you”ll see that what you like call my theory was promoted years ago by him. http://shapiro.bsd.uchicago.edu/
    Also here’s a good review of the subject that pops right up on Google: EVOLVING RESPONSIVELY: ADAPTIVE MUTATION
    http://www.micab.umn.edu/courses/8002/Rosenberg.pdf
    Remember Frank when you said, “I am interested in the research showing that my understanding of epigenetics is flawed,” Here’s your chance to read some and prove that you weren’t just using the usual deceptive commentary that your lot seems to thnik is a good debating ploy.

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