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Seeing the tree for the twigs
May 2007

chimp
When humans consider evolutionary history, we usually view the tree of life from the vantage point of our own tiny twig. We trace the hominid branch seven million years back in time — passing long-lost relatives along the way (our Neanderthal cousins, Great Aunt Lucy...) — until we reach the ancestor linking us with other primates and marvel, "Look how far we've come!" But just how impressive is our own evolution into a bipedal, big-brained, blabbering hominid? Now new research reveals that our own evolution may be more of a small hop in comparison to the leap taken by our closest living relative, the chimpanzee, and encourages us to take a broader view of the tree of life.

Where's the evolution?
This month, a team of geneticists from the University of Michigan led by Jianzhi Zhang announced a surprising discovery. They matched up corresponding sections of the human and chimp genomes and found more evidence of adaptation in chimps than in humans! The announcement inspired headlines generally relegated to the sports section: "Chimps lead evolutionary race!" "Step aside humans: Chimps have out-evolved you!" But of course, the underlying science is both more subtle and more complex than such headlines imply. Zhang's team studied almost 14,000 protein-coding genes and found 233 chimpanzee genes that seem to have been shaped by natural selection into more adaptive varieties. In contrast, only 154 human genes showed evidence of adaptive evolution. It seems then that, since our two lineages split, chimpanzee proteins have evolved to improve fitness more than human proteins have.

How do we know?
Anyone can take a look at the chimp and the human genomes online simply by Googling them, but the sequences themselves aren't very illuminating — screen after screen of As, Ts, Gs, and Cs, the bases of the genetic code. So how did Zhang and his colleagues sieve through this alphabet soup to figure out which genes within it underwent natural selection? Their method relies on a quirk of the genetic code.

The genetic code is redundant (e.g., both CGA and CGG code for the same amino acid in a protein). This means that some mutations (e.g., one that changes the last A in CGA to a G) will not have any effect at all on the protein produced. These changes are called synonymous mutations. Since synonymous mutations don't produce new protein varieties, they happen "underneath the radar" of natural selection. Other mutations are "non-synonymous" and do change the resulting protein. Since non-synonymous changes potentially affect protein function, they can be acted upon by natural selection. So, for example, if a non-synonymous mutation occurs and happens to increase a protein's ability to fight harmful bacteria, that mutation will be selected for and will increase in frequency in the population.

Zhang's team used this genetic quirk to seek out genes that had been targeted by natural selection. Since non-synonymous changes (i.e., protein-altering mutations) are visible to natural selection while synonymous changes are not, the team reasoned that "imbalanced genes" — those with unusually large numbers of non-synonymous changes in comparison to synonymous changes — had probably been acted upon by natural selection. At some point in the lineage's history, those non-synonymous mutations must have improved the protein's function, been favored by natural selection, and risen to high frequency. Using the macaque genome as a baseline, the team used computer programs to comb through the chimp and human genomes, identifying the targeted genes by their imbalance between non-synonymous and synonymous changes.

So how do we square chimps' highly-evolved proteins with common perceptions of humans and chimpanzees? After all, since the time of our common ancestor, humans have evolved larger brains, the capacity for speech, and the ability to walk upright. We've developed complex tools and civilizations and have spread throughout the world, while wild chimpanzees still live only in their native Africa and enjoy a lifestyle relatively similar to that of our common ancestor. "Surely it must be the other way around," one might think. "Surely human proteins have evolved more than chimp proteins. How else could our evolutionary history have carried us so far from our hominid origins?" There are at least two perspectives that can help make sense of this.

First, the Zhang team's research dealt only with the evolution of proteins — not with the effects those proteins have or with the genes that control those proteins. It's possible that much of human and chimp evolution can be chalked up to these other aspects of evolutionary change. A single change in a protein may generate a multitude of important changes in an organism's anatomy, physiology, and behavior. And even if the protein itself isn't altered at all, the evolution of the genes controlling that protein can produce a major trickledown effect, substantially changing the layout and other features of an organism's body. In short, it may be that the human characteristics that we recognize as so different from those of our ancestors (stature, cognitive ability, etc.) can be traced to evolution in just a few key genes. Although chimps may be more evolved than humans in terms of protein changes, many other aspects of the evolutionary change experienced by both lineages remain unaccounted for.


To find out how changes in control genes can affect an organism, learn more about the effects of mutations in our advanced tutorial on DNA and Mutations.

In addition, part of our surprise at the chimpanzee's more impressive protein evolution likely stems from our "people-centric" view of the world. As humans, we are familiar with our own species and see our own adaptations as unparalleled innovations that, we imagine, must be the result of major evolutionary change. But another organism might see it all differently. Imagine, for a moment, evolutionary history from the point of view of a plant. From the plant's perspective, humans and chimpanzees might seem like an undifferentiated sprout on the tree of life — a couple of hairy mammals with big heads — and after all, what's a little difference in brain size, compared to, say, the evolution that would be required to produce the plant's impressive chemically-defended sap, pollination system optimized to attract select pollinators, and aerodynamically-honed seedpods for maximum dispersal ability? A plant could be just as impressed with the evolutionary innovations that make it unique as we humans are with our own adaptations. And the same perspective-shifting exercise could be applied to any organism on the tree of life, including chimpanzees. In other words, we may be less impressed with chimp evolution simply because we’ve spent less time considering evolutionary history from their perspective, investigating the challenges they faced due to shifting habitats, changing climates, disease, and other organisms, and studying the breadth of adaptations that go into making a chimpanzee a chimpanzee.

A bird's-eye view of the tree of life makes it clear that evolution does not climb a ladder, leaving other organisms on lower rungs while pushing humans to the top. Instead evolutionary history forms a bushy tree with a myriad of evolving shoots, each shaped by unique episodes of natural selection, opportunities, and random events, which we have yet to fully appreciate. This more encompassing perspective reveals the true nature of our relationship to chimpanzees: they are not our evolutionary past, but are instead our modern cousins.

evolution does not climb a ladder


Read more about it

Primary literature:

  • Bakewell, M. A., Shi, P., and Zhang, J. (2007). More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences of the USA 104(18):7489-7494.
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News articles:

Understanding Evolution resources:

Discussion and extension questions

  1. What does it mean to evolve "more?" In what ways might humans have evolved "more" than chimps? In what ways might chimps have evolved "more" than humans?

  2. Review some background information on natural selection. Explain how a mutation that increases a protein's ability to fight harmful bacteria might spread through a population of chimpanzees. Make sure to include the concepts of variation, selection, and inheritance in your explanation.

  3. Do some research on the habitat, social structure, and lifestyle of the chimpanzee. Brainstorm a list of traits that natural selection might have acted upon during the evolutionary history of the chimpanzee's lineage.

  4. The article above claims that "chimpanzees are not our evolutionary past." Explain what this means. How are humans related to chimpanzees? Did we evolve from chimpanzees?

  5. Imagine that you are a scientist studying two species of fruit fly. You are particularly interested in a gene that helps the flies handle alcohol in the fermenting fruit they eat. You compare the gene in the two species to the probable sequence of the gene in their common ancestor. In both species, the gene has evolved. However, you discover that the evolutionary changes in Species A's gene are heavily biased towards non-synonymous changes, whereas changes in Species B's gene are more evenly distributed between the synonymous and non-synonymous varieties. How do you interpret these results?


Related lessons and teaching resources

  • Teach about how scientists study natural selection: This article for grades 9-12 describes the evolutionary history of lactose tolerance and how scientists have learned about the action of natural selection on this trait.

  • Teach about human and chimpanzee evolution: In this lesson for grades 9-12, students formulate explanations and models that simulate structural and biochemical data as they investigate the misconception that humans evolved from apes.

  • Teach about human ancestry: In this lesson for grades 9-12, students describe, measure, and compare cranial casts from contemporary apes, modern humans, and fossil hominids to discover some of the similarities and differences between these forms and to see the pattern leading to modern humans.


References

  • Bakewell, M. A., Shi, P., and Zhang, J. (2007). More genes underwent positive selection in chimpanzee evolution than in human evolution. Proceedings of the National Academy of Sciences of the USA 104(18):7489-7494.

  • Hopkin, M. (2007). Chimps lead evolutionary race. Nature 446:841.


Chimp photo by H. Vannoy Davis © California Academy of Sciences



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