Seeing The Branches for the Tree

There is a scientific picture waiting to be drawn. Someone has to do artistic justice to the evolutionary tree of life.

Back in 1837, Charles Darwin sketched out a tree of life in a notebook as a way to visualize his idea that different species share a common ancestor. In the generations since he published The Origin of Species, biologists have tried to draw trees that distill the actual relationships between living things.

As I wrote in 2012, the discovery of molecular biology gave scientists a better telescope for looking back through evolutionary history at the branches of the tree of life. Our DNA is an historical archive, storing a wealth of information about our kinship with the rest of life. In the 1970s, the biologist Carl Woese attempted the first sketch of the tree of life–a tree including the biggest groups of species. Woese argued that life consisted of three great branches–what he called domains. Those domains were typically referred to as bacteria, archaea, and eukaryotes–the last being our own.

Three-domain tree. Wikipedia. High-resolution version here:
The three-domain tree. See Wikipedia for a larger version

This picture is straightforward and bracing. Straightforward, because you can see its overall structure clearly. Bracing, because you can see your place in it. The length of the branches corresponds roughly to evolutionary distance. Humans and oak trees share the same tuft. For the most part, life’s diversity is microbial.

But this picture now appears to be wrong. A number of studies now suggest that the tree of life does not have three domains. Eukaryotes evolved from a lineage of archaea, which merged with a species of bacteria. In other words, we descend from a colossal hybridization. I blogged about some of this research in 2012, and this February, Ed Yong published a fantastic longer piece in Nautilus that included more recent research.

Today, three biologist offered an updated look at the evidence in Nature Reviews Microbiology. James McInerney, Mary O’Connell and Davide Pisani argue that the evidence in favor of the three-domain tree has been steadily diminishing, while the evidence for a merger has been gaining strength.

Maybe I have an overactive visual cortex, but when I read things like this, I think to myself, “What should I be seeing?” And perhaps I’m even more primed to ask that question because I’ve written textbooks about evolution, where pictures are invaluable for conveying the gist of complicated concepts. So I was intrigued that McInerney and his colleagues used this picture to illustrate their piece. (A bigger version is here.  That “chloroplast origin” is a wonderful tale in itself: how the algae that gave rise to plants gained the ability to capture sunlight for energy. For the full story, read Eating the Sun.)

McInerney et al Nat Rev Microbiology 2014
McInerney et al Nat Rev Microbiology 2014


It’s a beautiful picture, but…well, I’m not sure it quite works. It still has a three-ness to it, despite the fact that McInerney and his colleagues call on us to ditch the whole concept of three domains. Part of the problem may be that Darwin was only half right when he championed the tree of life as a metaphor for evolution. Mathematically speaking, a tree is a graph made of splitting lines. But the full story of evolution appears to be a graph that doesn’t just split, but also joins together into rings and other shapes (see this paper [pdf] for details). It  becomes harder to slice life up into neat groups when it keeps joining together.

I’ll probably use this figure in the next edition of my textbook, but I hope some visionary artist comes up with a new way to look at life.

27 thoughts on “Seeing The Branches for the Tree

  1. If you really want to understand the tree of life, read your Bible. It’s been proven to be not so fictitious as Darwin thought it was. Remember his father was a minister of the church, and he hated having God shoved down his throat, not an uncommon occurrence among children with fathers who were too harsh in their preaching and understanding of God.

    Evolution is no new theory. The Hindus had it down pat many millennia ago, but it is a theory developed by man only because he thinks he has to be perfect before he’s allowed to go to heaven. That’s not what God or the Bible teaches.

    Darwin’s THEORY has caused many people to think, “If we descended from apes, why not act like one?” and, “We all originated from pond scum, so if that’s all I am, what else do you expect from me?” I’ve heard too many young people and kids use these evolutionary theories as an excuse for their bad behavior, and lack of intention to clean it up.

    How much more respectable could we all be in our behaviors if we understood we were made by God, a God who doesn’t expect us to be perfect, just forgiven.

  2. All together now for Sylvia: “We are NOT descended from apes.”

    We have descended from a common ancestor to humans and apes. Except for politicians who are, in fact, descended from apes.

    1. You wrote, “All together now for Sylvia: ‘We are NOT descended from apes.’ We have descended from a common ancestor to humans and apes. Except for politicians who are, in fact, descended from apes.”

      That is not actually correct, either.

      We are not descended *from the species of apes alive today*. We have descended from a common ancestor to human (who are apes) and the other extant apes – and that common ancestor was, by the way, also an ape.

  3. First. Please be accurate in your statements if you’re going to post them so emphatically in a public venue. Darwin, as you point out, did not come up with the Theory of Evolution, simply the mechanism of Natural Selection. It’s also a stretch to even call that a theory these days, since scientists can legitimately stimulate and watch the process occurring. We also see it in the emergence of antibiotic-resistant bacteria, and the color change that has occurred in moth species as humans pollute their natural habitats. I know I’m not going to convince you here, but maybe someone else reading the comments will see and learn.

    The tree of life is a way to classify things according to their physiological and genetic origins. How do you explain things like comparative embryology, the common cell structure of all eukaryotic species, and the way that bacteria are evolving faster than we can find ways to kill them? In this case it’s a complete cop-out to say that it’s all God’s creation and the only people who will take that argument to heart at people who feel the same way. Most people want evidence and data. That’s the problem with this debate, one side cannot ever present what the other side needs to take them seriously.

    As to kids and their “pond scum” theories. If people were as well versed in adolescent psychology as they were in bible theory, they wouldn’t so quickly jump to conclusions about the impact that such teaching has on a child. Children will use any excuse they can to do the things you’re accusing…especially if they know that the adults around them will jump on the opportunity to shift blame off of their (lacking) parental skills and onto something else.. There is a difference between having faith, and walking around with your head in the sand. Any child who doesn’t understand the way the world works is at a serious disadvantage when compared to their peers.

    This is a situation where if you think you’re going to convince anyone of something by voicing your opinion on the internet, you’re going to have a bad time…but please at least get your facts straight.

  4. That was a very nice article. Sadly, people, like the above commenter, read it and need to add “god” to the subject. This was a nice, short little piece about evolution, and “god” doesn’t have a place here.

    I do wish people would keep religion where it belongs, in their church or in their homes – this is not the place for it. Lets, have information presented reasonably and logically, with references and supporting evidence, not with myths and fables.

  5. I dispute the premise that the theory of (r)evolution was caused by man’s belief he /she has to be perfect! The theory of (r)evolution is based on the recognition that (life’s) existence is based on change and/or developement. “God” is looking on…….

  6. Sylvia, Darwin’s father was a medical doctor – that pretty much sums up the factual material in your entire comment.

  7. Sylvia’s comment, although nicely worded, makes the usual error of referring to the THEORY of Evolution as something speculative, when in fact it is a fact. Richard Dawkins wrote a book called, “The Greatest Show on Earth,” which I highly recommend to anyone wanting to understand why Evolution is not “just a theory.”
    A second, common, erroneous assumption is that human beings can only derive a highly developed system of morality through religion in general, and the Bible in particular. This is untrue, and the best-known example of an advanced, non-theistic system of ethics and morality is called “Humanism,” which comes in many flavors, so there is one that any non-theist is sure to like.

    “The Greatest Show on Earth” — read it. “Humanism” — study it. You may not have anything to be forgiven for.

  8. It is a pity that you guys in the western world are blind to the things of the spirit and are usin your limited human knowledge to understand the wonderful work that our supreme God has accomplished. You’re looking for evidence of the involvement of God in creation when it abounds all around you. Long before science emerged prophets of God already filled with the Holy Spirit have been able to tell exactly what the world looked like. Before the age of Galileo, Isaiah already told us in his book that the earth is spherical and today science has confirmed it. When it comes to the things of the spirit, science will always lag behind and can only be late in finding out things that are already revealed to the spiritual person. Since man evolved from scum through bacteria why are there still bacteria today and why has bacteria not progressively evolved into things that are like humans. Over thousands over years bacteria has existed and have not evolved into what can be seen with the naked eyes but only through a microscope, why is it so?

    Please ask yourself some soul searching questions and you will come to the conclusion that God is actively involved in the work of creation. Do not be dumb but please be wise.

  9. The comments above demonstate the difference between science and religion. Science in an dynamic attempt to find a better, more accurate, answers. Religion is a set of static beliefs.

  10. First off, LincolnX, I love your last line. Thank you.

    Secondly, about Darwin: I think you are correct about Darwin’s father. As I was writing it, I kept thinking Darwin, himself, was the one who attended seminary, but when I looked it up, I discovered we were both wrong. The links below should clear a few things up. It seems he just didn’t believe in miracles, which included the creation story.

    However, I suggest you look beyond these two links, they were only the first two I found, and there is bound to be much more to the whole story of their education, religious upbringings and beliefs than those two links provide.

    Also, Kealey45 states that Darwin wasn’t teaching the theory of evolution, but simply the mechanism of natural selection. I’m sure Kealey is very well educated, but the fact is, Darwin did teach the theory of evolution. In more recent years, scientists have watered it down to make the theory of evolution more palatable to Christians by calling it the mechanism of natural selection.

    God does allow for natural selection and mutations based on the concept God Himself provided, which is called freedom of choice and the natural results of those choices. Genesis discusses that very concept, but if you want a more explicit discussion of what can happen when wrong choices are made, I suggest you read the epigraphea (I never know how to spell that word, but I think you get the idea) books, “Jubilees” and “The Book of Jasher”, both produced, not written by Ken Johnson, Th.D. He does provide little needed commentary. The results of experimentation using wrong choices (a freedom given them by God) concerning genetics, was the cause for the flood, which God provided to clean up Man’s hopeless mess. Scientists are now in the process of making those very same mistakes with their knowledge of genetics, and lack of knowledge of the lessons God teaches us in the Bible.

    By the way, scientists now agree there really was a world wide flood. Geologists, paleontologists, archeologists, cultural anthropologists, etc. have found too much evidence they can no longer deny. Of course, there are always those who will deny the truth in the face of all the facts. Those people are generally simply called stubborn and prideful. They don’t like to admit they might be wrong in their own beliefs. I had a grandmother who died of pure stubbornness. She didn’t want to go into a nursing home. She died four hours after she realized she was trapped, and no longer had any control over the decision. That’s what stubbornness can accomplish!

    Concerning teenagers having low opinions of themselves, I wasn’t talking just about teenagers. I have three children in their 40’s who have fallen for these same excuses for their bad behavior. They weren’t taught those ideas at home, so where did they get them? The oldest one isn’t nearly as bad about taking that attitude as the youngest one is.

    As for keeping the Bible and religion at home and in church, you are obviously ignorant of the fact that prayer was outlawed in schools in the 1970’s, only about 40 years ago, because of an atheist, Madeline O’Hare, who took it to the supreme court to get her way. By the way, atheism is in itself a religion, it just has a lot of idols they worship instead of the God who created us, mostly money, material things and self centeredness, and I have never run into a happy atheist. Madeline was herself a horribly miserable person in her lifetime.

    Another fact of U.S. history you’ve missed, for the first 200-300 years of this country’s history children learned to read in school with the Bible, and several other courses, none of them being religious courses (church was for that purpose), were based on what the Bible said as well. What’s more is, if you look at the dates when the Bible, prayer, teaching of Biblical creation, etc. were taken out of the schools and compare them to the falling morality of our society, you will find a great number of correlations between the two. There’s no such thing as coincidence. You’ve heard the saying, “What goes around, comes around.” You make bad choices, bad things happen to you.

    Concerning Richard Dawkins’ book, I’m a writer and an avid reader, and am fully aware anybody can write a book about anything, but that doesn’t mean it’s truth, and if there are enough gullible and/or uninformed people out there, it will be read and accepted as truth. I always make a point to read several sides of the same story so I will be well informed, and not so easily fall prey to writers who are just out there to make a buck or gain a little notoriety. Have you ever read the Bible, Phil, or anything connected to the Judeo-Christian beliefs? I suggest you do so, very studiously, before you read anything more in the area of science.

    Lastly, Chijioke, you are a very well read, intelligent and wise person. I commend you for it. I, too, am very aware of how far science is behind the truths spoken of in the Bible. Science has only continued to prove the Bible and its teachings to be correct. If more scientists read the Bible first, they could spend their time better by demonstrating and explaining those truths, rather than wasting it on trying to disprove it, and in their ignorance of the Bible teachings, end up proving it to be correct. You said it very well, and much better than I could.

    By the way, Patrick, where did revolution come from? If you’re saying Man revolted against God, because he thought he couldn’t be perfect, you completely missed my point. Man revolted against God, because he thought he was or could be as perfect as God. The theory of evolution (reincarnation) was developed when he discovered he couldn’t be as perfect as God in one lifetime, and therefore, needed more opportunities to gain that perfection. Satan has exactly the same beliefs. Where do you think the evolutionary theory came from? I might add, he has failed miserably in his beliefs, but for his efforts he’s going to be rewarded with eternity in the Lake of Fire, according to the book of Revelation.

  11. We must remember the number of scientists who built on Darwin’s theory in order to perpetuate a novel idea.

  12. Hi folks–Carl here. I just killed a comment that read, in its entirety, “With all due respect, Sylvia, shut up.” It’s fine to challenge people for their ideas, but insulting them or ordering them to be quiet is just not acceptable in these parts. I will continue to kill other rule-breaking comments with abandon.

  13. Theories of evolution were postulated by European scientists decades before Darwin precisely because the likes of Cuvier were starting to identify species that are now extinct. Darwin’s theory came along with a mechanism not in previous versions. If you’re going to talk about the history of evolutionary theories, Sylvia, you got that about as wrong as other things.

  14. Evolution in the sense of organisms changing over time is an ancient concept, independently arrived at by multiple cultures. The ancient Greeks had a version of it. So did the Hindus. So did many others. Multiple Victorian predecessors of Darwin played with the idea, including Darwin’s own grandfather Erasmus.

    But Darwin was the first to formulate a mechanism for this change that was testable. Darwin made the idea of evolution into a *theory*, in the scientific sense of that word.

  15. I’ve been enjoying Nicholas Money’s “The Amoeba in the Room”. One of the things he explains well is that horizontal gene transfer and symbiosis are more the norm than the exception in the microbial world. And since most of life is microbial that’s what we should be paying attention to. I wonder if the image you’re looking for should have a lot more co-mingling. A tree is such a macro-organismic image.

  16. Have you seen the picture used at It is intentionally weighted to make Eukarya look more important, so it doesn’t emphasise bacterial diversity like those you posted, but it’s much prettier! It uses the branching tree picture, but with branches reaching across the domains to represent the origins of eukaryotes and chloroplasts, and gene transfer between different microbial branches.

  17. Try out this one designed by Suzi Tucker Design out of Seattle for the exhibit “Emergence: A New View of Life’ Origin” at the New Mexico Museum of Natural History & Science in Albuqerque: She worked closely with our content providers from the Santa Fe Institute and we worked with Penelope Boston from New Mexico Tech to populate the tree with examples from New Mexico caves and other places.

  18. @Mimi Roberts – Suzi Tucker’s graphic is very nice and well thought out. Thanks for sharing that with the community.

  19. Is the correspondence between the length of the branches and time preserved I your new picture ? I wonder if the area of “leafs” could, somehow, correspond to the relative abundances of species within each domain.

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