Common Ancestry, Nested Hierarchies, and Parsimony

| By on Letters to the Duchess

In this series, we explore the genetic evidence that indicates humans became a separate species as a substantial population, rather than descending uniquely from an ancestral pair.

In the last post in this series, we introduced the concept of mutations that are shared between species as one line of evidence for common ancestry. In the example we examined, we saw how the deletion of the same DNA letter was present in three primate species: humans, chimpanzees, and orangutans. If indeed these three species share a common ancestral population, then this pattern is easily explained – the mutation occurred in their shared ancestral population, became more common within that population over time, eventually became the only version of that gene in the population, and then was subsequently inherited by the branching populations that went on to become present-day humans, chimpanzees and orangutans. The alternative hypothesis, that humans, chimpanzees, and orangutans do not share a common ancestral population, requires that this precise mutation occurred three times in three separate populations, and replaced the functional version of the gene three times over in those three populations. While such a possibility is rare, for a single gene such a series of improbable events might occur three times independently. In the absence of any other data, a geneticist would rightly hesitate somewhat; though highly suggestive of shared ancestry, such a data set would be too small to draw a firm conclusion.

Of course, in this era of genome sequencing, we now have complete DNA sequences for humans and other great apes to compare to one another. One finding that may be a surprise to non-biologists is that genomes change much, much more slowly than languages do. As we have seen, a mere 1600 years is enough to bring about modern English and Frisian from a common ancestral language – languages that, for all their similarities, are mutually unintelligible to each other despite a relatively recent separation. The human and chimpanzee genomes, on the other hand, are nearly identical to each other. If you restrict the comparison to the small fraction of the genome that contains gene sequences, the two species are over 99% identical to each other. If you expand the analysis to include all sequences (even ones that do not appear to have a sequence-specific function, or repetitive DNA that seems to accumulate in genomes over time), the number hardly shifts, dropping to about 95% identical. To put that in perspective, the human and chimpanzee genomes are more identical to each other than many alternative readings of certain passages in the New Testament, as minor as many of those differences are. And just as no one doubts that two New Testament fragments 95% identical to each other are in fact related through a process of (imperfect) copying, so too it is a significant stretch to argue that the human genome is not related to the chimpanzee genome, given such a high level of shared identity between them. On the whole, our genome and the chimpanzee genome have the features one would predict for slightly modified descendants of a common ancestral genome.

The nose knows (or at least it once did)

Having the complete genome sequences for a variety of great apes makes looking for additional shared mutations a trivial exercise, and it is no exaggeration to say that there are thousands of examples that could be used. One study examining shared mutations in great apes focused on a class of genes used for the sense of smell, known as olfactory receptor genes. The proteins encoded by these genes are present on the cells of the nasal epithelium—the surface of our noses—where they bind to molecules in the air. This binding sends nerve impulses to our brains, which, in specific combinations, we perceive as smells. Primates, as it turns out, have lost a number of genes in this category—and as we saw for the GULO enzyme, we share identical mutations in some of these genes with other primates. For example, in the data set from this study, twelve identical mutations were found to be shared between primates in a particular pattern (shown in red in the diagram below).

Three of these mutations are shared between humans and chimpanzees only; a further three are shared between humans, chimpanzees and gorillas; and a further six identical mutations are shared between humans, chimpanzees, gorillas and orangutans. This pattern is readily explained by the following: the common ancestral population of all four species has six mutations that occurred prior to the lineage leading to orangutans branched off; three more that occurred before the lineage leading to gorillas branched off; and another three that occurred before the lineages leading to humans and chimpanzees separated. In this model, there are no repeated identical mutation events in separate lineages—every mutation happens only once. Note also what we do notobserve—shared mutations that are not part of this pattern. While the researchers found other mutated olfactory genes, none of these mutations were shared, but rather present in only one species. Put another way, in this data set if we see a mutation shared between humans and gorillas, we see those exact mutations in chimpanzees without fail. Likewise, if we see a mutation shared between humans and orangutans, we see those exact mutations in gorillas and chimpanzees, again without fail. The shared mutations make a precise pattern that is exactly the pattern we expect if indeed these species share common ancestral populations that progressively divided into four lineages—a pattern known as a nested hierarchy.

Consider the alternative hypothesis for this data set—that humans, chimpanzees, gorillas, and orangutans do not share common ancestral populations. In order to explain the above data, we would have to postulate a long list of improbable events:

  • Six identical mutations occur independently in all four species, and each mutation replaces the functional version of the gene in each species.
  • Three identical mutations occur independently in gorillas, chimpanzees, and humans, but not in orangutans. Each mutation replaces the functional version of the gene in the three affected species.
  • Three identical mutations occur independently in chimpanzees and humans, but not in gorillas or orangutans. Each mutation replaces the functional version of the gene in both species.
  • As you can see, the alternative explanation requires numerous, identical mutation events in unrelated species that just happen to match one specific pattern out of thousands of possible patterns – the one pattern predicted by shared ancestry. And once you consider the thousands of shared mutations that conform to this pattern across the great apes, it becomes apparent just how strong the evidence for common ancestry is, and how strained the alternatives are. In scientific terms, common ancestry is a much simpler explanation, requiring far fewer events, and producing the observed pattern as a consequence of the mechanism rather than by chance. In other words, common ancestry is a vastly more satisfactory explanation for what we observe in nature than the alternative hypothesis that humans do not share ancestors with other apes.

    As an aside, a third hypothesis is that the pattern of shared mutations is in fact the result of common design, rather than common descent. This option is one that I am often asked about. This hypothesis, however, is even more strained than postulating independent mutation events. In this case, we would have to postulate that, for reasons unknown to us, a designer placed these sequences into these four species with their mutations already in place, and thus not able to function as olfactory receptors. Additionally, the sequences were placed in precisely the pattern that common ancestry would produce. (Alternatively, the designer may have placed functional sequences into these four species but then chose to inactivate them in a specific pattern consistent with common ancestry). While such a possibility cannot be absolutely ruled out, it is very much an ad hoc explanation. After all, we know what these genes are for (contributing to the sense of smell), and we know from the mutations that they carry that they cannot perform that function. Similarly, we know that the GULO enzyme is for making vitamin C, and we know that it is non-functional in primates. The idea that God placed these mutations (and thousands of other examples) into these species in a pattern matching what common ancestry would produce - when in fact common ancestry is false - is something that I find theologically problematic.

    Common ancestry, then, is by far and away the most parsimonious explanation for the data we see. And as I sometimes comment to my students, it’s possible to view common descent as God’s ordained mechanism for bringing about new species. In this sense, descent is the design.

    Variation, populations, and speciation

    What then, does this have to do with the central question of this series? The first consideration is that if humans indeed are the product of evolution and share ancestors with other species, we would expect that the process was mediated through populations, since evolution is a population-level phenomenon. Beyond this, however, is a way to use related species to estimate population size during the speciation process. In the above examples, each mutation completely replaced the functional version of the gene in the population before the lineages separated. In some cases, however, we would expect lineages to separate with genetic variation present for a given gene – i.e. with two or more alleles present in the population when it is separated into two lineages. Once we have a clear picture of how species are related to each other, we can search for genes that happened to have two or more variants during a speciation event, and use such genes to estimate population sizes for the resulting species – a topic we will explore in the next post in this series.




    Venema, Dennis. "Common Ancestry, Nested Hierarchies, and Parsimony" N.p., 12 Feb. 2015. Web. 22 February 2018.


    Venema, D. (2015, February 12). Common Ancestry, Nested Hierarchies, and Parsimony
    Retrieved February 22, 2018, from /blogs/dennis-venema-letters-to-the-duchess/adam-eve-and-human-population-genetics-part-6-common-ancestry-nested-hierarchies-and-parsimony

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    About the Author

    Dennis Venema

    Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia and Fellow of Biology for BioLogos. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

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