Trees of Life: Choose Your Diversity

By Carl Zimmer | February 11, 2009 3:16 pm

I am hanging out at the airport, having just missed my flight to Raleigh, but free wireless makes it just an extra office. I’ve just read a few complaints on my post about visualizing the tree of life. Some commenters are not pleased that the tree I illustrated the post with does a grave disservice to the overwhelming diversity of the bacterial world. It is certainly true that bacteria (and archaea) are staggeringly diverse. In a spoonful of soil there may be 10,000 species of microbes. By comparison, there are only about 5,000 mammal species. A lot of the diversity in microbes is ancient, since they’ve been around a lot longer than mammals, or even animals.

That being said, it’s important to bear in mind that there is no tree that includes all 1.8 million known species on the tree of life. Or even one percent of the branches. The biggest tree out there that I know of has 13,533 branches, and it’s just a tree showing how plants are related to each other. It’s likely that there are five or ten times more species waiting to be discovered. The mostly unknown diversity of microbes may kick that figure even higher.

So the best we have to settle for right now are stick figure drawings. The illustration I used was produced a few years ago by David Hillis at the University of Texas and his colleagues. Of all the evolutionary trees that include branches from all the major groups of living things, Hillis’s has the most species. (If there’s a bigger one out there, just let me know.) There indeed a lot of animals, plants, and fungi on his tree, but until recently, they dominated the genetic databases that researchers use to build such trees. That’s changing fast now, fortunately.

For those who want things put in better perspective, the best I can offer you is a modified version of a tree I’ll be showing tomorrow at my Darwin Day talk. The original tree comes from the interactive Tree of Life site. It’s based on all the species whose genomes have been fully sequenced. The iTOL scientists analyze a select group of genes that show little sign of having been swapped between species. Here, all the eukaryotes (us, fungi, plants, protozoans) are in the red section of the outer circle. The blue are bacteria, the green archaea (a separate branch of microbes). There’s some debate over the methods the scientists used to generate this tree, and the few hundred branches are pretty paltry. But it definitely conveys the deep diversity among the microbes, and the surprisingly small distance between you and a Portobello mushroom.


CATEGORIZED UNDER: Evolution, Writing Elsewhere

Comments (9)

  1. Scott Belyea

    the surprisingly small distance between you and a Portobello mushroom.

    That is interesting, and effectively conveyed.

    Mind you, if the fungus in question were brushed with olive oil and grilled, the distance between us would diminish even further …

  2. That is not even remotely the biggest tree of life. People have made trees of all the available rRNA sequences from cultured and uncultured organisms and that can be upwards of 1,000,000 sequences. I have seen trees with > 100,000 tips. They may not be perfectly constructed trees, but they have been made. Some of these can be found at the various rRNA databases out there … will try to post a link

  3. R. E. Love

    It’s great to see this sort of information get out to the interested public rather than squirreled away in some journal few but scientists read. There are some things that need considering, though.
    One, if time rather than genetic divergence were the radius (all the examples are alive today, save possibly a very recent extinction or two) all the lines would come to the same outer circle, that is, have the same radius. This would make a quite different appearing (if much harder to read) graphic, perhaps conveying a quite different impression.
    Even more so, the proportion of species tested in each group. If a million+ or so insects, 60 thousand or so fish, etc. were in the sample, the distance between the Portobello and us would be greatly expanded (to the detriment of gourmands), far more than the approximately 4/5 of bacteria in this graph. To my knowledge, no one knows whether there actually are more kinds of bacteria than all other living things, an impression quite obvious in this graphic (and quite possibly true!) Bacteria have the advantage of containing a single strand bacterial chromosome of limited length, relatively easy to sequence in entirety. This is a bias that certainly colors the picture violet. Actually, those doing this sort of work find evidence of new bacteria and some other things as well by sampling the oceanic broth, many of the living sources never even found.
    Lastly, in a cladogram (which this graphic is), it is convention (sometimes ignored, thankfully) that puts the less divergent group’s branch to the side of the nearest ancestral relative. The result of this puts Darwinopithecus way off to the right of Portobello (left, if you are reading this in Australia). This convention is no way based on real information. Each node can be rotated either way with the exact same cladistic information. A moment’s thought will demonstrate this: the horizontal lines give no information besides connecting the radial branches, otherwise, how would each endpoint be exactly the same distance from its neighbor as every other neighboring pair? Rotating the node just to the right of the fungi would put my bearded friend only three places off from that tasty mushroom, and rotating its basal node puts it adjacent to the nearest mushroom collector. It’s so easy to manipulate a graphic to portray a bias, in this case, emphasizing the old “Ladder of Life” idea by putting humans at the far end, equivalent to the peak of evolution (shudder). Personally, I like crickets there.

  4. Would it not be more realistic to picture the plant of life as an organism with roots as well as branches? Much of bios is in the soil rather than the atmosphere. The evolution of earth-bound species could be shown with the oldest progenitors close to the trunk and the later ones further out on the root system. Additionally, using the subterranean portion of the tree would provide a wider canvas to illustrate the development of present day life.

  5. t I found a 10 year old file from the original Ribosomal Database Project on my computer and then I looked for the same thing on the web. And I found it.

    Go to;O=A.

    And look for the if you want a post script giant tree or

    SSU_Prok.newick.Z if you want one in an older tree format.

    This has something like 6000 tips I think (not at my real computer right now so not so sure). But this is over 10 years old and I am certain someone has made many much larger ones since. The plant and animal people talk big and certainly they do great things. But the microbial people have been building bigger trees for some time …

  6. Hernanie P. Nacino



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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.


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